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annotate msconvert.xml @ 13:9337a492ebab draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 73cce4134ad971568ac8e557df97bab93ff24d4d
author galaxyp
date Fri, 25 Apr 2025 10:03:13 +0000
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9337a492ebab planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit 73cce4134ad971568ac8e557df97bab93ff24d4d
galaxyp
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1 <tool id="msconvert" name="msconvert" version="@VERSION@.6" profile="@PROFILE_VERSION@">
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5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
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2 <description>Convert and/or filter mass spectrometry files</description>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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3 <macros>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
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4 <import>msconvert_macros.xml</import>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
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5 </macros>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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6 <xrefs>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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7 <xref type="bio.tools">msconvert</xref>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
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8 </xrefs>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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9 <requirements>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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10 <container type="docker">chambm/pwiz-skyline-i-agree-to-the-vendor-licenses:@FULL_VERSION@</container>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
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11 </requirements>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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12 <stdio>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
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13 <regex match="Error writing run" source="stderr" level="fatal" description="Could not convert. Check stderr." />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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14 </stdio>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
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15 <expand macro="msconvertCommand" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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16 <inputs>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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17 <param format="mzml,mzxml,mz5,mgf,ms2,thermo.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" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
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18 <expand macro="msconvertInputParameters" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
galaxyp
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19 </inputs>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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20 <expand macro="msconvertOutput" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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21 <tests>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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22 <expand macro="msconvert_tests" />
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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23 </tests>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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24 <help><![CDATA[
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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25 **What it does**
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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26
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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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.
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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29 You can view the original documentation here_.
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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31 .. _here: http://proteowizard.sourceforge.net/tools/msconvert.html
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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32 ]]></help>
5e94d5403baf planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/msconvert commit dade2a055b8b1bd4b3c177638e833eb2a6c65196
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33 <expand macro="citations" />
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34 </tool>