Mercurial > repos > iracooke > protk_proteogenomics

annotate mzid_to_protxml.xml @ 0:956bfab63005 draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:36:03 -0400
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956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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1 <tool id="mzid_to_protxml" name="mzIdentML to protXML" version="1.0.1">
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2 <description>Convert mzIdentML to protXML</description>
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4 <requirements>
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5 <container type="docker">iracooke/protk-1.4.3</container>
956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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6 <requirement type="package" version="1.4.3">protk</requirement>
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7 <requirement type="package" version="2.2.29">blast+</requirement>
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8 </requirements>
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10 <command>
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11 mzid_to_protxml.rb $mzid_file
956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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13 -o $output
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14 </command>
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16 <stdio>
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17 <exit_code range="1:" level="fatal" description="Failure" />
956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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18 </stdio>
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20 <inputs>
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22 <param name="mzid_file" type="data" format="mzid" multiple="false" label="Proteomics Search Results" help="A ProtXML file produced by Protein Prophet"/>
956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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24 </inputs>
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956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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26 <outputs>
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27 <data format="protxml" name="output" />
956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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28 </outputs>
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956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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31 <tests>
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32 <test>
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33 <param name="mzid_file" value="PeptideShaker_tiny.mzid" format="mzid"/>
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34 <output name="output" format="protxml">
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35 <assert_contents>
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36 <has_text text="JEMP01000061" />
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37 </assert_contents>
956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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38 </output>
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39 </test>
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40 </tests>
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42 <help>
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44 **What it does**
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46 Roughly converts mzIdentML to protXML.
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956bfab63005 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/protk-proteogenomics/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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48 At the present time, the conversion is really only designed to work with mzIdentML files produced by PeptideShaker and to produce protXML files suitable for input to protk proteogenomics tools.
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51 </help>
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53 </tool>