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1 <tool id="protxml_to_table_1" name="ProtXML to Table" version="1.1.0">
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2 <requirements>
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3 <container type="docker">iracooke/protk-1.4.1</container>
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4 <requirement type="package" version="1.4">protk</requirement>
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5 </requirements>
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6
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7 <description>Converts a ProtXML file to a table</description>
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8
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9 <command>
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10 protxml_to_table.rb
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11 $invert_probs
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13 $input_file
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14 -o $output
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15 </command>
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16
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17 <inputs>
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18
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19 <param format="protxml" name="input_file" type="data" label="ProtXML File to Convert"/>
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20 <param name="invert_probs" type="boolean" label="Print inverted probabilities (ie 1-p instead of p)" truevalue="--invert-probabilities" falsevalue=""/>
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21 </inputs>
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22
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23
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24 <outputs>
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25 <data format="tabular" name="output" />
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26 </outputs>
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27
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28 <tests>
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29 <!-- Just test that the tool runs and produces vaguely correct output -->
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30 <test>
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31 <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml" format="protxml"/>
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32 <output name="output" format="tabular">
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33 <assert_contents>
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34 <has_text text="AVQKYLTAHEQSK" />
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35 </assert_contents>
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36 </output>
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37 </test>
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38 </tests>
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39
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40
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41 <help>
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42
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43 **What it does**
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44
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45 Converts a ProtXML file to a tab separated table
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46
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47 </help>
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48
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49 </tool>
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