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1 <tool id="MergeScaffold" name="Merge Scaffold">
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2 <description></description>
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3 <command interpreter="python">MergeFiles.py $input1 $input2 $input3 $baitfile $merged \$INSTALL_RUN_PATH/</command>
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4 <requirements>
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5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement>
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6 </requirements>
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7 <inputs>
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8 <param format="txt" name="input1" type="data" label="Scaffold Output 1"/>
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9 <param format="txt" name="input2" type="data" label="Scaffold Output 2"/>
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10 <param format="txt" name="input3" type="data" label="Scaffold Output 3" optional = "true"/>
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11 <param format="txt" name="baitfile" type="data" label="baitfile"/>
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12 </inputs>
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13 <outputs>
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14 <data format="txt" name="merged" label="Merged Scaffold Report"/>
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15 </outputs>
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16 <stdio>
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17 <regex match="Error|error"
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18 source="stdout"
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19 level="fatal"
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20 description="Unknown error"/>
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21 <regex match="Error|error"
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22 source="stderr"
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23 level="fatal"
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24 description="Unknown error"/>
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25 <regex match="Error: bad bait"
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26 source="stdout"
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27 level="fatal"
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28 description="Error: bad bait"/>
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29 </stdio>
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30 <tests>
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31 <test>
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32 <param name="input" value="fa_gc_content_input.fa"/>
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33 <output name="out_file1" file="fa_gc_content_output.txt"/>
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34 </test>
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35 </tests>
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36 <help>
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37 Query CRAPome
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38 -------------
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39 This program will read in a SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions (e.g. "P00533" or "EGFR_HUMAN"), query the CRAPome database (v1.1) http://crapome.org, and return a file specifying the prevalence of each protein in the CRAPome.
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40
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41 **1) Input File**
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42 SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions.
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43
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44 **2) Species**
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45 Please specify species. Supported species are Human and Yeast.
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46 </help>
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47 </tool> |
