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comparison msconvert.xml @ 16:545054b15d7c draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 2cce57c0b3173029ce8fb3e7b4607b3913581dfd
author galaxyp
date Sun, 24 Mar 2024 11:13:43 +0000
parents 6153e8ada1ee
children ab6c14374bc0
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15:6153e8ada1ee 16:545054b15d7c
1 <tool id="msconvert" name="msconvert" version="@VERSION@.2"> 1 <tool id="msconvert" name="msconvert" version="@VERSION@.3">
2 <description>Convert and/or filter mass spectrometry files</description> 2 <description>Convert and/or filter mass spectrometry files</description>
3 <macros> 3 <macros>
4 <import>msconvert_macros.xml</import> 4 <import>msconvert_macros.xml</import>
5 </macros> 5 </macros>
6 <requirements> 6 <xrefs>
7 <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container> 7 <xref type="bio.tools">msconvert</xref>
8 </requirements> 8 </xrefs>
9 <stdio> 9 <requirements>
10 <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." /> 10 <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>
11 </stdio> 11 </requirements>
12 <expand macro="msconvertCommand" /> 12 <stdio>
13 <inputs> 13 <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." />
14 <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" /> 14 </stdio>
15 <expand macro="msconvertInputParameters" /> 15 <expand macro="msconvertCommand" />
16 </inputs> 16 <inputs>
17 <expand macro="msconvertOutput" /> 17 <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" />
18 <tests> 18 <expand macro="msconvertInputParameters" />
19 <expand macro="msconvert_tests" /> 19 </inputs>
20 </tests> 20 <expand macro="msconvertOutput" />
21 <help> 21 <tests>
22 <expand macro="msconvert_help" /> 22 <expand macro="msconvert_tests" />
23 </help> 23 </tests>
24 <expand macro="citations" /> 24 <help><![CDATA[
25 **What it does**
26
27 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.
28
29 You can view the original documentation here_.
30
31 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
32 ]]></help>
33 <expand macro="citations" />
25 </tool> 34 </tool>