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Add bio.tools for msconvert #748

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merged 4 commits into from
Mar 24, 2024
Merged

Add bio.tools for msconvert #748

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f8ccd13
Add bio.tools for msconvert
bebatut Mar 11, 2024
62bee50
Merge branch 'master' into msconvert-biotools
bgruening Mar 12, 2024
b3ef969
Merge branch 'master' into msconvert-biotools
bebatut Mar 18, 2024
79947db
Try to fix linting
bebatut Mar 18, 2024
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2 changes: 1 addition & 1 deletion tools/msconvert/.shed.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -12,4 +12,4 @@ long_description: |
Main web site: http://www.proteowizard.org
remote_repository_url: https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert
type: unrestricted

homepage_url: http://proteowizard.sourceforge.net/tools.shtml
57 changes: 33 additions & 24 deletions tools/msconvert/msconvert.xml
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Original file line number Diff line number Diff line change
@@ -1,25 +1,34 @@
<tool id="msconvert" name="msconvert" version="@[email protected]">
<description>Convert and/or filter mass spectrometry files</description>
<macros>
<import>msconvert_macros.xml</import>
</macros>
<requirements>
<container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>
</requirements>
<stdio>
<regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." />
</stdio>
<expand macro="msconvertCommand" />
<inputs>
<param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" />
<expand macro="msconvertInputParameters" />
</inputs>
<expand macro="msconvertOutput" />
<tests>
<expand macro="msconvert_tests" />
</tests>
<help>
<expand macro="msconvert_help" />
</help>
<expand macro="citations" />
<tool id="msconvert" name="msconvert" version="@[email protected]">
<description>Convert and/or filter mass spectrometry files</description>
<macros>
<import>msconvert_macros.xml</import>
</macros>
<xrefs>
<xref type="bio.tools">msconvert</xref>
</xrefs>
<requirements>
<container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>
</requirements>
<stdio>
<regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." />
</stdio>
<expand macro="msconvertCommand" />
<inputs>
<param format="mzml,mzxml,mz5,mgf,ms2,thermo.raw,raw,wiff,wiff.tar,agilentbrukeryep.d.tar,agilentmasshunter.d.tar,brukerbaf.d.tar,brukertdf.d.tar,watersmasslynx.raw.tar" name="input" type="data" label="Input unrefined MS data" />
<expand macro="msconvertInputParameters" />
</inputs>
<expand macro="msconvertOutput" />
<tests>
<expand macro="msconvert_tests" />
</tests>
<help><![CDATA[
**What it does**

Converts mass spectrometry (MS) files: proprietary MS vendor formats can be converted to open MS formats (mzML, mzXML, MGF, MS1/MS2) and open formats can be converted to other open formats. Additional options such as filtering and/or precursor recalculation are available.

You can view the original documentation here_.

.. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
]]></help>
<expand macro="citations" />
</tool>
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