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CRAPomeQuery.xml |
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| diff -r 4d47d78b193a -r 7a0b06a1cabd CRAPomeQuery.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/CRAPomeQuery.xml Mon Apr 18 12:17:05 2016 -0400 |
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| @@ -0,0 +1,48 @@ +<tool id="CRAPomeQuery" name="Query CRAPome"> + <description></description> + <command interpreter="python">CRAPomeQuery.py $input $species $CrapomeFile \$INSTALL_RUN_PATH/</command> + <requirements> + <requirement type="set_environment">INSTALL_RUN_PATH</requirement> + </requirements> + <inputs> + <param format="txt" name="input" type="data" label="Prey File or single column list"/> + <param type="select" name="species" label="Species"> + <option value="HUMAN">Human</option> + <option value="YEAST">Yeast</option> + </param> + </inputs> + <outputs> + <data format="txt" name="CrapomeFile" label="CRAPome File"/> + </outputs> + <stdio> + <regex match="Error|error" + source="stdout" + level="fatal" + description="Unknown error"/> + <regex match="Error|error" + source="stderr" + level="fatal" + description="Unknown error"/> + <regex match="Error: bad bait" + source="stdout" + level="fatal" + description="Error: bad bait"/> + </stdio> + <tests> + <test> + <param name="input" value="fa_gc_content_input.fa"/> + <output name="out_file1" file="fa_gc_content_output.txt"/> + </test> + </tests> + <help> +Query CRAPome +------------- +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. + +**1) Input File** +SAINT formatted *Prey* file or a single column list (no column name) of Uniprot accessions. + +**2) Species** +Please specify species. Supported species are Human and Yeast. + </help> +</tool> \ No newline at end of file |