Mercurial > repos > iracooke > xtandem

annotate tandem_to_pepxml.xml @ 18:bbef168551fe draft default tip

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit aa789ac01391258aff7a819ebf64a7cbc46730c9
author galaxy-australia
date Wed, 18 May 2022 23:50:58 +0000
parents 29e2df3edf11
children
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0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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1 <tool id="tandem_to_pepxml_1" name="Tandem to pepXML" version="1.1.1">
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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2 <description>Converts a tandem result file to pepXML</description>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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3 <requirements>
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iracooke
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4 <container type="docker">iracooke/protk-1.4.3</container>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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5 <requirement type="package" version="1.4.3">protk</requirement>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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6 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement>
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7 </requirements>
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8 <stdio>
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9 <exit_code range="1:" level="fatal" description="Failure" />
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10 </stdio>
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iracooke
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11 <command>
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12 tandem_to_pepxml.rb $input_file -o $output
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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13 </command>
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iracooke
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15 <inputs>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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16 <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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17 </inputs>
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0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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19 <outputs>
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iracooke
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20 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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21 </outputs>
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iracooke
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22 <tests>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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23 <!-- Just test that the tool runs and produces vaguely correct output -->
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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24 <test>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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25 <param name="input_file" value="tandem_to_pepxml_test.tandem" format="tandem"/>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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26 <output name="output" format="raw_pepxml">
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iracooke
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27 <assert_contents>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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28 <has_text text="SQVFQLESTFDV" />
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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29 </assert_contents>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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30 </output>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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31 </test>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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32 </tests>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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33 <help>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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34 Convert X!Tandem results to pepXML
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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35 </help>
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36 </tool>