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1 <tool id="CRAPomeQuery" name="Query CRAPome">
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2 <description></description>
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3 <command interpreter="python">CRAPomeQuery.py $input $species $fasta_db $CrapomeFile \$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="input" type="data" label="Prey File or single column list"/>
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9 <param type="select" name="species" label="Species">
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10 <option value="HUMAN">Human</option>
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11 <option value="YEAST">Yeast</option>
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12 </param>
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13 <param type="data" name="fasta_db" format="fasta" label="Provide Uniprot Fasta database" optional="true"/>
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14 </inputs>
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15 <outputs>
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16 <data format="txt" name="CrapomeFile" label="CRAPome File"/>
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17 </outputs>
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18 <stdio>
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19 <regex match="TypeError"
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20 source="stderr"
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21 level="fatal"
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22 description="Error: Check input file."/>
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23 <regex match="Error|error"
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24 source="stdout"
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25 level="fatal"
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26 description="Unknown error"/>
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27 <regex match="Error|error"
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28 source="stderr"
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29 level="fatal"
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30 description="Unknown error"/>
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31 </stdio>
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32 <tests>
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33 <test>
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34 <param name="input" value="fa_gc_content_input.fa"/>
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35 <output name="out_file1" file="fa_gc_content_output.txt"/>
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36 </test>
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37 </tests>
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38 <help>
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39 Query CRAPome
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40 -------------
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41 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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42
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43 **1) Input File**
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44
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45 SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions.
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46
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47 **2) Species**
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48
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49 Please specify species. Supported species are Human and Yeast.
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50
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51 **3) Uniprot Fasta Database**
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52
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53 A uniprot database can be provided that will be used to get gene names.
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54 </help>
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55 </tool> |
