Mercurial > repos > bornea > query_crapome
comparison CRAPomeQuery.xml @ 1:7a0b06a1cabd draft
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| author | bornea |
|---|---|
| date | Mon, 18 Apr 2016 12:17:05 -0400 |
| parents | |
| children | 9c72c51d858d |
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| 0:4d47d78b193a | 1:7a0b06a1cabd |
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| 1 <tool id="CRAPomeQuery" name="Query CRAPome"> | |
| 2 <description></description> | |
| 3 <command interpreter="python">CRAPomeQuery.py $input $species $CrapomeFile \$INSTALL_RUN_PATH/</command> | |
| 4 <requirements> | |
| 5 <requirement type="set_environment">INSTALL_RUN_PATH</requirement> | |
| 6 </requirements> | |
| 7 <inputs> | |
| 8 <param format="txt" name="input" type="data" label="Prey File or single column list"/> | |
| 9 <param type="select" name="species" label="Species"> | |
| 10 <option value="HUMAN">Human</option> | |
| 11 <option value="YEAST">Yeast</option> | |
| 12 </param> | |
| 13 </inputs> | |
| 14 <outputs> | |
| 15 <data format="txt" name="CrapomeFile" label="CRAPome File"/> | |
| 16 </outputs> | |
| 17 <stdio> | |
| 18 <regex match="Error|error" | |
| 19 source="stdout" | |
| 20 level="fatal" | |
| 21 description="Unknown error"/> | |
| 22 <regex match="Error|error" | |
| 23 source="stderr" | |
| 24 level="fatal" | |
| 25 description="Unknown error"/> | |
| 26 <regex match="Error: bad bait" | |
| 27 source="stdout" | |
| 28 level="fatal" | |
| 29 description="Error: bad bait"/> | |
| 30 </stdio> | |
| 31 <tests> | |
| 32 <test> | |
| 33 <param name="input" value="fa_gc_content_input.fa"/> | |
| 34 <output name="out_file1" file="fa_gc_content_output.txt"/> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help> | |
| 38 Query CRAPome | |
| 39 ------------- | |
| 40 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. | |
| 41 | |
| 42 **1) Input File** | |
| 43 SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions. | |
| 44 | |
| 45 **2) Species** | |
| 46 Please specify species. Supported species are Human and Yeast. | |
| 47 </help> | |
| 48 </tool> |