Mercurial > repos > iracooke > xtandem

annotate tandem_to_pepxml.xml @ 15:0faaab4f192a draft

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:47:05 -0400
parents 9d6e0ad4d600
children 29e2df3edf11
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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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9d6e0ad4d600 Docker support and update for protk 1.4
iracooke
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7 </requirements>
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iracooke
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8 <command>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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9 tandem_to_pepxml.rb $input_file -o $output
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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10 </command>
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0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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12 <inputs>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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13 <param name="input_file" type="data" format="tandem" multiple="false" label="Input File" help="X!Tandem results file"/>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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14 </inputs>
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0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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16 <outputs>
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iracooke
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17 <data format="raw_pepxml" metadata_source="input_file" name="output" label="${input_file.display_name}.pepXML" />
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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18 </outputs>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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19 <tests>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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20 <!-- 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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21 <test>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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22 <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
iracooke
parents: 14
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23 <output name="output" format="raw_pepxml">
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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24 <assert_contents>
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iracooke
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25 <has_text text="SQVFQLESTFDV" />
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
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26 </assert_contents>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
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27 </output>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
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28 </test>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
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29 </tests>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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30 <help>
0faaab4f192a planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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31 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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32 </help>
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33 </tool>