Mercurial > repos > iracooke > tpp_prophets

annotate protxml_to_table.xml @ 15:0746a2ae9e04 draft

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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:45:24 -0400
parents d90c8bc10a9c
children
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15
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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1 <tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.1">
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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2 <description>Converts a ProtXML file to a table</description>
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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>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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5 <requirement type="package" version="1.4.3">protk</requirement>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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6 </requirements>
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iracooke
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7 <command>
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iracooke
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8 protxml_to_table.rb
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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9 $invert_probs
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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10 $input_file
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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11 -o $output
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iracooke
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12 </command>
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iracooke
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13 <inputs>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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14 <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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15 <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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16 </inputs>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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17 <outputs>
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18 <data format="tabular" name="output" />
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
parents: 14
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19 </outputs>
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20 <tests>
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iracooke
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21 <!-- Just test that the tool runs and produces vaguely correct output -->
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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22 <test>
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iracooke
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23 <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml" format="protxml"/>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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24 <output name="output" format="tabular">
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
iracooke
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25 <assert_contents>
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26 <has_text text="AVQKYLTAHEQSK" />
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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27 </assert_contents>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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28 </output>
0746a2ae9e04 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
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29 </test>
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30 </tests>
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31 <help>
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32 **What it does**
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33
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34 Converts a ProtXML file to a tab separated table
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35
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36 </help>
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37 </tool>