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Björn Grüning bgruening University of Freiburg Freiburg (Germany) orcid.org/0000-0002-3079-6586

aidanbudd/bosc2015 16

Using BOSC2015 unconference sessions on building successful open source bioinformatics communities to write an open collaborative article

ASaiM/framework 12

Open-source opinionated Galaxy-based framework for microbiota analysis

BackofenLab/GraphClust-2 10

A pipeline for structural clustering of RNA secondary structures

afgane/galaxy-tools-playbook 9

A ready-to-use Ansible playbook for the Galaxy Tools role

65MO/Galaxy-E 5

Towards a Galaxy for Ecology

bgruening/argparse2galaxy 2

Convert a python argparse defintion in a Galaxy Tool XML

bgruening/bcbb 1

Useful bioinformatics code, primarily in Python and R

bgruening/bioconda_biocontainers_talk 1

BioConda & BioContainers

anatskiy/galaxy 0

Data intensive science for everyone.

AndreasSko/docker-galaxy-stable 0

:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.

pull request commentgalaxy-iuc/standards

Modify recommended test data sets size

Ok, I added some initial thoughts here: https://github.com/bgruening/test-data-registry/blob/main/README.md

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pull request commentbgruening/docker-galaxy-stable

Bump to 21.09

Mh, it seems we need to update python somewhere?

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UUID and proper headers

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pull request commentgalaxy-iuc/standards

Modify recommended test data sets size

I should :( I will make this a priority for me next week. I have this here as an initial idea: https://github.com/bgruening/test-data-registry

(Nextflow and Snakemake would be interested to join this effort)

I will write my ideas down.

gallardoalba

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issue openedgalaxyproject/galaxy

Connection issue in the workflow editor (Bowtie)

Describe the bug

image

I think both tools should be able to be connected.

Related: https://help.galaxyproject.org/t/bowtie2-output-data-type-not-recognised-in-workflow-designer/7323

Galaxy Version and/or server at which you observed the bug Galaxy Version: 21.09 on EU and ORG

Expected behavior

Both tools should be connectable.

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pull request commentNordicESMhub/galaxy-tools

cdo Galaxy Tools

installed on EU

annefou

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pull request commentgalaxy-iuc/standards

Modify recommended test data sets size

We test dependencies and in update, we also look if a tool update changes the results in an expected way.

We ensure that we're still building correctly command lines that result in the expected result. Not more, not less.

1. It's not our job to make sure the underlying tool is correct. Yes we can report issues we find, but we shouldn't waste our time on this or be expected to be some sort of external CI.

2. All the bugs we've found in bedtools for instance were present in tiny test data.

Agreed. Where do we disagree here ;) The question is what have expected results, how can you define them, and what size of inputs we need. There are just plenty of tools that do need test data of > 500kb and a few even bigger than 1MB. The trick to moving them to the bgruening repo, because they are not applying to IUC guidelines is not good and an artificial barrier for tool devs. And we waste a lot of time reducing test data to under 1MB, its the number 1 hurdle of tools devs imho.

I do agree to reduce test data as much as possible and I think we should have a recommendation, enforcing this and giving no way out is problematic imho - reducing 1MB to 500kb is just increasing the pain.

How big is big enough to be realistic anyway ? There's no realistic limit on that, is there ?

As small as possible is the current and good recommendation. No one is talking about big or large.

I guess before we change the limit I would like to understand the reason for a limit at first. The old reason I remember is the size of the github repo, wich I think is a technical limitation that we should fix in otherways.

The number one thing is test runtime.

When did we had problems with runtime? We had several problems with file size and always need to remind people to shrink their data, but runtime? Maybe with mothur and 120 tools?

Many users would like to understand how an input needs to look like and how the output for example looks.

I disagree with the premise, but I would like to point out that this is much clearer with synthetic test data than with large "realistic" data.

I do not talk about realistic data, as in real-world data, but data that at least creates a meaningful output (aka not empty ;)). This ends up very often as synthetic data, after many many hours of fiddling. I have done this too many times e.g. for GalaxyP, this is not fun.

The TDT is actually going on step further and explain parameters etc ... but that is then the next level.

The TDT has zero information to go on about explaining the parameter, beyond what is in the tool interface anyway. Why does it matter if the test data is large for this purpose? How do you want the TDT to explain to users what is important about the test data, where it came from etc? Also, which of the many tests that a good wrapper has is the one the TDT should explain? Again, that's another discussion we can have about a demo mode. Using test data for this seems wrong to me.

And we have and had a plan for that.

I agree that users should be able to run the test from the interface if they want to know that the tool actually works, but what's the point of that test case being large ? I feel like you're concluding that seeing test data makes users understand the test data and why it's been chosen. I think that is a huge jump, where the TDT approach has no way of taking the user by the hand and little way of taking the intermediate steps. The TDT idea of re-using test cases we already have sounds good in theory, but I don't think it is helpful in practice.

If that's the reason for large test data I think we're hampering our testing efforts for very little benefit.

Sorry, I'm not talking about large test data. As small as possible. We see that we can create good tests with 1MB for 90% (?) of the tools, and maybe 99% with 1-10MB? We could look over the tools that we have if we want to have proper data.

My button line is to not change the test-data recommendation, but get the URI idea that we are talking about for 5 years implemented instead.

gallardoalba

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pull request commentBMCV/galaxy-image-analysis

Added a new tool and updated an existing tool

Thanks! No clue how the new OSX does that. Conda needs to work or Docker, maybe that is also the problem?

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Add container cdo:2.0.0. **Hash**: cdo:2.0.0 **Packages**: - cdo=2.0.0 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest **For** : - cdo_info.xml - cdo_operations.xml Generated with Planemo.

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Merge pull request #2031 from dockerhub-toolshed/cdo-2.0.0 Add container cdo:2.0.0.

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PR merged BioContainers/multi-package-containers

Add container cdo:2.0.0.

Hash: cdo:2.0.0

Packages:

  • cdo=2.0.0 Base Image:quay.io/bioconda/base-glibc-busybox-bash:latest

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  • cdo_info.xml
  • cdo_operations.xml

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add CDO tools

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draft cdo tool

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cdo information operators

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added another netCDF for cdo tests

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tested implemented cdo operations

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add new cdo operators

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format xmls

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diff lines for tests with cdo

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add more options for cdo and tests

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bug was a typo with optional

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deal with cdo options

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PR merged NordicESMhub/galaxy-tools

cdo Galaxy Tools
  • [x] cdo information operators (info, sinfo, diff)
  • [x] cdo file operations (copy, merge, etc.)
  • [x] cdo selection (select,, selname, delname, etc.
  • [x] cdo modification (setattribute)
  • [x] cdo statistics (min, max, standard deviation, etc.)
  • [x] cdo expression (expr)
  • [x] cdo interpolation (such as ml2pl, intlevel, etc.)
  • [x] cdo transformation (such as sp2gp or gp2sp)
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pull request commentgalaxy-iuc/standards

Modify recommended test data sets size

To me the purpose of test data is to make sure we generate a valid command line for the tool. If you look at the test data in Galaxy you won't find a single realistic set of test data ... because that's not the purpose of these tests.

In IUC and on other repos are a lot of good, valid test data. And we test more than just the command-line. We test dependencies and in update, we also look if a tool update changes the results in an expected way. At least I do this, when possible.

I doubt that just giving users some test data is enough to understand the input parameters of a tool. You could list some example data in the tool, that seems like a good idea, but I don't think we want to use these as tests.

It's not about the input parameters. Its about the general function of the tool. Many users would like to understand how an input needs to look like and how the output for example looks. I end up recommending using the test data to users to understand how inputs need to be formatted or simply to confirm the tool is working. We can link other test data, or we can reuse the test-data that either way needs to be crafted by the tool author. Why repeating the work here? The TDT is actually going on step further and explain parameters etc ... but that is then the next level.

I guess before we change the limit I would like to understand the reason for a limit at first. The old reason I remember is the size of the github repo, wich I think is a technical limitation that we should fix in otherways.

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pull request commentNordicESMhub/galaxy-tools

cdo Galaxy Tools

You can move the sdtio to macro and on file pathos not quoted. That's theast things I can see.

annefou

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Pull request review commentNordicESMhub/galaxy-tools

cdo Galaxy Tools

+<macros>+    <xml name="stat_selection">+        <param name="stat" type="select" label="Select statistical function" multiple="false">+            <option value="min">minimum</option>+            <option value="max">maximum</option>+            <option value="sum">sum</option>+            <option value="mean">mean</option>+            <option value="avg">average</option>+            <option value="var">variance</option>+            <option value="std">standard deviation</option>+        </param>+    </xml>+    <xml name="cdo_option">+        <conditional name="option_type">+            <param name="add_opt" type="select" label="Provide cdo options" multiple="false">+                <option value="-a">Generate an absolute time axis (-a)</option>+                <option value="--cmor">CMOR conform NetCDF output (--cmor)</option>+                <option value="-f">-Output format (-f format)</option>+                <option value="-g">-g grid</option>+                <option value="-gf">-g grid filename</option>+                <option value="-M">-Indicate that the I/O streams have missing values (-M)</option>+                <option value="-m">Set the default missing value. Default is-9e+33 (-m missval)</option>+                <option value="--percentile">Percentile method (--percentile method)</option>+                <option value="--reduce_dim">Reduce NetCDF dimensions (--reduce_dim)</option>+                <option value="-R">Convert GRIB1 data from reduced to regular grid (-R)</option>+                <option value="--seed">Seed for a new sequence of pseudo-random numbers (--seed seed)</option>+                <option value="--sortname">Alphanumeric sorting of NetCDF parameter names (--sortname)</option>+                <option value="-r">Generate a relative time axis (-r)</option>+            </param>+            <when value="-a"/>+            <when value="--cmor"/>+            <when value="-f">+                <param name="output_format" type="text" label="Output format"/>+            </when>+            <when value="-g">+                <param name="grid" type="text" label="Grid" help="(option -g grid)"/>+            </when>+            <when value="-gf">+                <param name="gridfile" type="data" label="Grid file" help="(option -g gridfile)" format="txt"/>+            </when>+            <when value="-M"/>+            <when value="-m">+                <param name="missval" type="float" value="-9e+33" label="Set the default missing value"/>+            </when>+            <when value="--percentile">+                <param name="percentile" type="select" label="Percentile method">+                    <option value="nrank">nrank</option>+                    <option value="nist">nist</option>+                    <option value="rtype8">rtype8</option>+                    <option value="numpy">numpy</option>+                    <option value="numpy_lower">numpy_lower</option>+                    <option value="numpy_higher">numpy_higher</option>+                    <option value="numpy_nearest">numpy_nearest</option>+                </param>+            </when>+            <when value="--reduce_dim"/>+            <when value="-R"/>+            <when value="--seed">+                <param name="seed" type="float" value="0.0" label="Seed for a new sequence of pseudo-random numbers"/>+            </when>+            <when value="--sortname"/>+            <when value="-r"/>+        </conditional>+    </xml>+    <xml name="cdo_operator">+        <conditional name="operator">+            <param name="opt" type="select" label="Select cdo operator" multiple="false">+                <option value="copy">copy (Copy datasets)</option>+                <option value="cat">cat (Concatenate datasets)</option>+                <option value="replace">replace (Replace variables)</option>+                <option value="duplicate">duplicate (Duplicates a dataset)</option>+                <option value="mergegrid">mergegrid (Merge grid)</option>+                <option value="merge">merge (Merge datasets with different fields)</option>+                <option value="mergetime">mergetime (Merge datasets sorted by date and time)</option>+                <option value="splitcode">splitcode (Split code numbers)</option>+                <option value="splitparam">splitparam (Split parameter identifiers)</option>+                <option value="splitname">splitname (Split variable names)</option>+                <option value="splitlevel">splitlevel (Split levels)</option>+                <option value="splitgrid">splitgrid (Split grids)</option>+                <option value="splitzaxis">splitzaxis (Split z-axes)</option>+                <option value="splittabnum">splittabnum (Split parameter table numbers)</option>+                <option value="splithour">splithour (Split hours)</option>+                <option value="splitday">splitday (Split days)</option>+                <option value="splitseas">splitseas (Split seasons)</option>+                <option value="splityear">splityear (Split years)</option>+                <option value="splityearmon">splityearmon (Split in years and months)</option>+                <option value="splitmon">splitmon (Split months)</option>+                <option value="splitsel">splitsel (Split time selection)</option>+                <option value="distgrid">distgrid (Distribute horizontal grid)</option>+                <option value="collgrid">collgrid (Collect horizontal grid)</option>+                <option value="select">select (Select all fields with parameters in a user given list.)</option>+                <option value="delete">delete (Delete all fields with parameters in a user given list.)</option>+                <option value="selname">selname (Select parameters by name)</option>+                <option value="delname">delname (Delete parameters by name)</option>+                <option value="seltimestep">seltimestep (Select timesteps)</option>+                <option value="sellonlatbox">sellonlatbox (Select a latitude/longitude box)</option>+                <option value="invertlat">invertlat (Invert latitudes)</option>+                <option value="addc">addc (Add a constant)</option>+                <option value="subc">subc (Substract a constant)</option>+                <option value="mulc">mulc (Multiply with a constant)</option>+                <option value="divc">divc (Divide with a constant)</option>+                <option value="expr">expr (Evaluate expressions)</option>+                <option value="ml2pl">ml2pl (Model to pressure level interpolation)</option>+                <option value="ml2hl">ml2hl (Model to height level interpolation)</option>+                <option value="intlevel">intlevel (Linear level interpolation)</option>+                <option value="sp2gp">sp2gp (Spectral to gridpoint)</option>+                <option value="gp2sp">gp2sp (Gridpoint to spectral)</option>+                <option value="ens">Ensemble statistics</option>+                <option value="zon">Zonal statistics</option>+                <option value="tim">Time statistics</option>+                <option value="vert">Vertical statistics</option>+                <option value="day">Daily statistics</option>+                <option value="year">Yearly statistics</option>+                <option value="mon">Monthly statistics</option>+                <option value="seas">Seasonal statistics</option>+                <option value="fld">Statistical values over a field</option>+                <option value="add">Add two fields </option>+                <option value="sub">Subtract two fields </option>+                <option value="mul">Multiply two fields </option>+                <option value="div">Divide two fields </option>+                <option value="min">Minimum of two fields </option>+                <option value="max">Maximum of two fields </option>+		<option value="setattribute">Set/modifiy attributes</option>+            </param>+            <when value="copy">+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="cat">+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="replace">+                <param name="add_file" type="data" multiple="true" min="0" max="2" label="Additional input file" format="netcdf"/>+            </when>+            <when value="duplicate">+                <param name="ndup" type="integer" label="Number of duplicates, default is 2." value="2"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="mergegrid">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="merge">+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="mergetime">+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitcode">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitparam">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitname">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitlevel">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitgrid">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitzaxis">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splittabnum">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splithour">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitday">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitseas">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splityear">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splityearmon">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitmon">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitsel">+                <param name="nset" type="integer" value="0" label="Number of input timesteps for each output file"/>+                <param name="noffset" type="integer" optional="true" label="Number of input timesteps skipped before the first timestep range (optional)"/>+                <param name="nskip" type="integer" optional="true" label="Number of input timesteps skipped between timestep ranges (optional)"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="distgrid">+                <param name="nx" type="integer" value="1" label="Number of regions in x direction, or number of pieces for unstructured grids"/>+                <param name="ny" type="integer" label="Number of regions in y direction" value="1"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="collgrid">+                <param name="nx" type="integer" label="Number of regions in x direction" optional="true"/>+                <param name="names" type="text" label="Comma-separated list of variable names" optional="true"/>+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="select">+                <param name="params" type="text" value="" label="Parameters for selection"/>+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="delete">+                <param name="params" type="text" label="Parameters for deletion"/>+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="selname">+                <param name="params" type="text" value="" label="Parameters for selection"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="delname">+                <param name="params" type="text" value="" label="Parameters for selection"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="seltimestep">+                <param name="params" type="text" value="" label="Timesteps for selection"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="sellonlatbox">+                <param name="params" type="text" value="" label="Parameters for latitude/longitude box in the form of lon1,lon2,lat1,lat2)"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="invertlat">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="addc">+                <param name="const_value" type="float" label="Constant value" value="1"/>

You could, this is possible. But not needed. It's ok as it is.

annefou

comment created time in a day

PullRequestReviewEvent

pull request commentNordicESMhub/galaxy-tools

cdo Galaxy Tools

Yes. I can backport it to EU then.

annefou

comment created time in a day

Pull request review commentNordicESMhub/galaxy-tools

cdo Galaxy Tools

+<macros>+    <xml name="stat_selection">+        <param name="stat" type="select" label="Select statistical function" multiple="false">+            <option value="min">minimum</option>+            <option value="max">maximum</option>+            <option value="sum">sum</option>+            <option value="mean">mean</option>+            <option value="avg">average</option>+            <option value="var">variance</option>+            <option value="std">standard deviation</option>+        </param>+    </xml>+    <xml name="cdo_option">+        <conditional name="option_type">+            <param name="add_opt" type="select" label="Provide cdo options" multiple="false">+                <option value="-a">Generate an absolute time axis (-a)</option>+                <option value="--cmor">CMOR conform NetCDF output (--cmor)</option>+                <option value="-f">-Output format (-f format)</option>+                <option value="-g">-g grid</option>+                <option value="-gf">-g grid filename</option>+                <option value="-M">-Indicate that the I/O streams have missing values (-M)</option>+                <option value="-m">Set the default missing value. Default is-9e+33 (-m missval)</option>+                <option value="--percentile">Percentile method (--percentile method)</option>+                <option value="--reduce_dim">Reduce NetCDF dimensions (--reduce_dim)</option>+                <option value="-R">Convert GRIB1 data from reduced to regular grid (-R)</option>+                <option value="--seed">Seed for a new sequence of pseudo-random numbers (--seed seed)</option>+                <option value="--sortname">Alphanumeric sorting of NetCDF parameter names (--sortname)</option>+                <option value="-r">Generate a relative time axis (-r)</option>+            </param>+            <when value="-a"/>+            <when value="--cmor"/>+            <when value="-f">+                <param name="output_format" type="text" label="Output format"/>+            </when>+            <when value="-g">+                <param name="grid" type="text" label="Grid" help="(option -g grid)"/>+            </when>+            <when value="-gf">+                <param name="gridfile" type="data" label="Grid file" help="(option -g gridfile)" format="txt"/>+            </when>+            <when value="-M"/>+            <when value="-m">+                <param name="missval" type="float" value="-9e+33" label="Set the default missing value"/>+            </when>+            <when value="--percentile">+                <param name="percentile" type="select" label="Percentile method">+                    <option value="nrank">nrank</option>+                    <option value="nist">nist</option>+                    <option value="rtype8">rtype8</option>+                    <option value="numpy">numpy</option>+                    <option value="numpy_lower">numpy_lower</option>+                    <option value="numpy_higher">numpy_higher</option>+                    <option value="numpy_nearest">numpy_nearest</option>+                </param>+            </when>+            <when value="--reduce_dim"/>+            <when value="-R"/>+            <when value="--seed">+                <param name="seed" type="float" value="0.0" label="Seed for a new sequence of pseudo-random numbers"/>+            </when>+            <when value="--sortname"/>+            <when value="-r"/>+        </conditional>+    </xml>+    <xml name="cdo_operator">+        <conditional name="operator">+            <param name="opt" type="select" label="Select cdo operator" multiple="false">+                <option value="copy">copy (Copy datasets)</option>+                <option value="cat">cat (Concatenate datasets)</option>+                <option value="replace">replace (Replace variables)</option>+                <option value="duplicate">duplicate (Duplicates a dataset)</option>+                <option value="mergegrid">mergegrid (Merge grid)</option>+                <option value="merge">merge (Merge datasets with different fields)</option>+                <option value="mergetime">mergetime (Merge datasets sorted by date and time)</option>+                <option value="splitcode">splitcode (Split code numbers)</option>+                <option value="splitparam">splitparam (Split parameter identifiers)</option>+                <option value="splitname">splitname (Split variable names)</option>+                <option value="splitlevel">splitlevel (Split levels)</option>+                <option value="splitgrid">splitgrid (Split grids)</option>+                <option value="splitzaxis">splitzaxis (Split z-axes)</option>+                <option value="splittabnum">splittabnum (Split parameter table numbers)</option>+                <option value="splithour">splithour (Split hours)</option>+                <option value="splitday">splitday (Split days)</option>+                <option value="splitseas">splitseas (Split seasons)</option>+                <option value="splityear">splityear (Split years)</option>+                <option value="splityearmon">splityearmon (Split in years and months)</option>+                <option value="splitmon">splitmon (Split months)</option>+                <option value="splitsel">splitsel (Split time selection)</option>+                <option value="distgrid">distgrid (Distribute horizontal grid)</option>+                <option value="collgrid">collgrid (Collect horizontal grid)</option>+                <option value="select">select (Select all fields with parameters in a user given list.)</option>+                <option value="delete">delete (Delete all fields with parameters in a user given list.)</option>+                <option value="selname">selname (Select parameters by name)</option>+                <option value="delname">delname (Delete parameters by name)</option>+                <option value="seltimestep">seltimestep (Select timesteps)</option>+                <option value="sellonlatbox">sellonlatbox (Select a latitude/longitude box)</option>+                <option value="invertlat">invertlat (Invert latitudes)</option>+                <option value="addc">addc (Add a constant)</option>+                <option value="subc">subc (Substract a constant)</option>+                <option value="mulc">mulc (Multiply with a constant)</option>+                <option value="divc">divc (Divide with a constant)</option>+                <option value="expr">expr (Evaluate expressions)</option>+                <option value="ml2pl">ml2pl (Model to pressure level interpolation)</option>+                <option value="ml2hl">ml2hl (Model to height level interpolation)</option>+                <option value="intlevel">intlevel (Linear level interpolation)</option>+                <option value="sp2gp">sp2gp (Spectral to gridpoint)</option>+                <option value="gp2sp">gp2sp (Gridpoint to spectral)</option>+                <option value="ens">Ensemble statistics</option>+                <option value="zon">Zonal statistics</option>+                <option value="tim">Time statistics</option>+                <option value="vert">Vertical statistics</option>+                <option value="day">Daily statistics</option>+                <option value="year">Yearly statistics</option>+                <option value="mon">Monthly statistics</option>+                <option value="seas">Seasonal statistics</option>+                <option value="fld">Statistical values over a field</option>+                <option value="add">Add two fields </option>+                <option value="sub">Subtract two fields </option>+                <option value="mul">Multiply two fields </option>+                <option value="div">Divide two fields </option>+                <option value="min">Minimum of two fields </option>+                <option value="max">Maximum of two fields </option>+		<option value="setattribute">Set/modifiy attributes</option>+            </param>+            <when value="copy">+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="cat">+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="replace">+                <param name="add_file" type="data" multiple="true" min="0" max="2" label="Additional input file" format="netcdf"/>+            </when>+            <when value="duplicate">+                <param name="ndup" type="integer" label="Number of duplicates, default is 2." value="2"/>

default 2 should also be moved into help or removed entirely

annefou

comment created time in a day

Pull request review commentNordicESMhub/galaxy-tools

cdo Galaxy Tools

+<macros>+    <xml name="stat_selection">+        <param name="stat" type="select" label="Select statistical function" multiple="false">+            <option value="min">minimum</option>+            <option value="max">maximum</option>+            <option value="sum">sum</option>+            <option value="mean">mean</option>+            <option value="avg">average</option>+            <option value="var">variance</option>+            <option value="std">standard deviation</option>+        </param>+    </xml>+    <xml name="cdo_option">+        <conditional name="option_type">+            <param name="add_opt" type="select" label="Provide cdo options" multiple="false">+                <option value="-a">Generate an absolute time axis (-a)</option>+                <option value="--cmor">CMOR conform NetCDF output (--cmor)</option>+                <option value="-f">-Output format (-f format)</option>+                <option value="-g">-g grid</option>+                <option value="-gf">-g grid filename</option>+                <option value="-M">-Indicate that the I/O streams have missing values (-M)</option>+                <option value="-m">Set the default missing value. Default is-9e+33 (-m missval)</option>+                <option value="--percentile">Percentile method (--percentile method)</option>+                <option value="--reduce_dim">Reduce NetCDF dimensions (--reduce_dim)</option>+                <option value="-R">Convert GRIB1 data from reduced to regular grid (-R)</option>+                <option value="--seed">Seed for a new sequence of pseudo-random numbers (--seed seed)</option>+                <option value="--sortname">Alphanumeric sorting of NetCDF parameter names (--sortname)</option>+                <option value="-r">Generate a relative time axis (-r)</option>+            </param>+            <when value="-a"/>+            <when value="--cmor"/>+            <when value="-f">+                <param name="output_format" type="text" label="Output format"/>+            </when>+            <when value="-g">+                <param name="grid" type="text" label="Grid" help="(option -g grid)"/>+            </when>+            <when value="-gf">+                <param name="gridfile" type="data" label="Grid file" help="(option -g gridfile)" format="txt"/>+            </when>+            <when value="-M"/>+            <when value="-m">+                <param name="missval" type="float" value="-9e+33" label="Set the default missing value"/>+            </when>+            <when value="--percentile">+                <param name="percentile" type="select" label="Percentile method">+                    <option value="nrank">nrank</option>+                    <option value="nist">nist</option>+                    <option value="rtype8">rtype8</option>+                    <option value="numpy">numpy</option>+                    <option value="numpy_lower">numpy_lower</option>+                    <option value="numpy_higher">numpy_higher</option>+                    <option value="numpy_nearest">numpy_nearest</option>+                </param>+            </when>+            <when value="--reduce_dim"/>+            <when value="-R"/>+            <when value="--seed">+                <param name="seed" type="float" value="0.0" label="Seed for a new sequence of pseudo-random numbers"/>+            </when>+            <when value="--sortname"/>+            <when value="-r"/>+        </conditional>+    </xml>+    <xml name="cdo_operator">+        <conditional name="operator">+            <param name="opt" type="select" label="Select cdo operator" multiple="false">+                <option value="copy">copy (Copy datasets)</option>+                <option value="cat">cat (Concatenate datasets)</option>+                <option value="replace">replace (Replace variables)</option>+                <option value="duplicate">duplicate (Duplicates a dataset)</option>+                <option value="mergegrid">mergegrid (Merge grid)</option>+                <option value="merge">merge (Merge datasets with different fields)</option>+                <option value="mergetime">mergetime (Merge datasets sorted by date and time)</option>+                <option value="splitcode">splitcode (Split code numbers)</option>+                <option value="splitparam">splitparam (Split parameter identifiers)</option>+                <option value="splitname">splitname (Split variable names)</option>+                <option value="splitlevel">splitlevel (Split levels)</option>+                <option value="splitgrid">splitgrid (Split grids)</option>+                <option value="splitzaxis">splitzaxis (Split z-axes)</option>+                <option value="splittabnum">splittabnum (Split parameter table numbers)</option>+                <option value="splithour">splithour (Split hours)</option>+                <option value="splitday">splitday (Split days)</option>+                <option value="splitseas">splitseas (Split seasons)</option>+                <option value="splityear">splityear (Split years)</option>+                <option value="splityearmon">splityearmon (Split in years and months)</option>+                <option value="splitmon">splitmon (Split months)</option>+                <option value="splitsel">splitsel (Split time selection)</option>+                <option value="distgrid">distgrid (Distribute horizontal grid)</option>+                <option value="collgrid">collgrid (Collect horizontal grid)</option>+                <option value="select">select (Select all fields with parameters in a user given list.)</option>+                <option value="delete">delete (Delete all fields with parameters in a user given list.)</option>+                <option value="selname">selname (Select parameters by name)</option>+                <option value="delname">delname (Delete parameters by name)</option>+                <option value="seltimestep">seltimestep (Select timesteps)</option>+                <option value="sellonlatbox">sellonlatbox (Select a latitude/longitude box)</option>+                <option value="invertlat">invertlat (Invert latitudes)</option>+                <option value="addc">addc (Add a constant)</option>+                <option value="subc">subc (Substract a constant)</option>+                <option value="mulc">mulc (Multiply with a constant)</option>+                <option value="divc">divc (Divide with a constant)</option>+                <option value="expr">expr (Evaluate expressions)</option>+                <option value="ml2pl">ml2pl (Model to pressure level interpolation)</option>+                <option value="ml2hl">ml2hl (Model to height level interpolation)</option>+                <option value="intlevel">intlevel (Linear level interpolation)</option>+                <option value="sp2gp">sp2gp (Spectral to gridpoint)</option>+                <option value="gp2sp">gp2sp (Gridpoint to spectral)</option>+                <option value="ens">Ensemble statistics</option>+                <option value="zon">Zonal statistics</option>+                <option value="tim">Time statistics</option>+                <option value="vert">Vertical statistics</option>+                <option value="day">Daily statistics</option>+                <option value="year">Yearly statistics</option>+                <option value="mon">Monthly statistics</option>+                <option value="seas">Seasonal statistics</option>+                <option value="fld">Statistical values over a field</option>+                <option value="add">Add two fields </option>+                <option value="sub">Subtract two fields </option>+                <option value="mul">Multiply two fields </option>+                <option value="div">Divide two fields </option>+                <option value="min">Minimum of two fields </option>+                <option value="max">Maximum of two fields </option>+		<option value="setattribute">Set/modifiy attributes</option>+            </param>+            <when value="copy">+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="cat">+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="replace">+                <param name="add_file" type="data" multiple="true" min="0" max="2" label="Additional input file" format="netcdf"/>+            </when>+            <when value="duplicate">+                <param name="ndup" type="integer" label="Number of duplicates, default is 2." value="2"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="mergegrid">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="merge">+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="mergetime">+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitcode">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitparam">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitname">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitlevel">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitgrid">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitzaxis">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splittabnum">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splithour">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitday">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitseas">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splityear">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splityearmon">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitmon">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="splitsel">+                <param name="nset" type="integer" value="0" label="Number of input timesteps for each output file"/>+                <param name="noffset" type="integer" optional="true" label="Number of input timesteps skipped before the first timestep range (optional)"/>+                <param name="nskip" type="integer" optional="true" label="Number of input timesteps skipped between timestep ranges (optional)"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="distgrid">+                <param name="nx" type="integer" value="1" label="Number of regions in x direction, or number of pieces for unstructured grids"/>+                <param name="ny" type="integer" label="Number of regions in y direction" value="1"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="collgrid">+                <param name="nx" type="integer" label="Number of regions in x direction" optional="true"/>+                <param name="names" type="text" label="Comma-separated list of variable names" optional="true"/>+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="select">+                <param name="params" type="text" value="" label="Parameters for selection"/>+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="delete">+                <param name="params" type="text" label="Parameters for deletion"/>+                <param name="add_file" type="data" multiple="true" min="0" label="Additional input file" format="netcdf"/>+            </when>+            <when value="selname">+                <param name="params" type="text" value="" label="Parameters for selection"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="delname">+                <param name="params" type="text" value="" label="Parameters for selection"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="seltimestep">+                <param name="params" type="text" value="" label="Timesteps for selection"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="sellonlatbox">+                <param name="params" type="text" value="" label="Parameters for latitude/longitude box in the form of lon1,lon2,lat1,lat2)"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="invertlat">+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="addc">+                <param name="const_value" type="float" label="Constant value" value="1"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="subc">+                <param name="const_value" type="float" label="Constant value" value="1"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="mulc">+                <param name="const_value" type="float" label="Constant value" value="1"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="divc">+                <param name="const_value" type="float" label="Constant value" value="1"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="expr">+                <param name="params" type="text" value="" label="Expression for evaluation"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="ml2pl">+                <param name="params" type="text" value="" label="Pressure levels (comma separated)"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="ml2hl">+                <param name="params" type="text" value="" label="Height levels (comma separated)"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="intlevel">+                <param name="params" type="text" value="" label="Levels (comma separated)"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="sp2gp">+                <param name="trunc" type="integer" optional="true" value="" label="New spectral resolution"/>+                <param name="add_file" type="data" optional="true" value="" label="Additional input file" format="netcdf"/>+            </when>+            <when value="gp2sp">+                <param name="trunc" type="integer" optional="true" label="New spectral resolution"/>+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>+            </when>+            <when value="ens">+                <expand macro="stat_selection" />+                <param name="add_file" type="data" optional="true" label="Additional input file" format="netcdf"/>

add_file could be its own macro

annefou

comment created time in a day

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