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* Add bio.tools for msconvert * Try to fix linting --------- Co-authored-by: Björn Grüning <[email protected]>
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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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