Mercurial > repos > rsajulga > proteomic_cravat_score_and_annotate
changeset 3:7f319af8c5b3 draft
Uploaded
| author | rsajulga |
|---|---|
| date | Thu, 17 May 2018 22:32:51 -0400 |
| parents | 676c8be98be4 |
| children | 5e0334dc65f0 |
| files | cravat_submit.xml |
| diffstat | 1 files changed, 8 insertions(+), 6 deletions(-) [+] |
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--- a/cravat_submit.xml Thu May 17 22:32:25 2018 -0400 +++ b/cravat_submit.xml Thu May 17 22:32:51 2018 -0400 @@ -1,6 +1,6 @@ <tool id="cravat_submit" name="CRAVAT Submit, Check, and Retrieve" version="0.1.0"> <description>Submits, checks for, and retrieves data for cancer annotation</description> - <command interpreter="python">cravat_submit.py $input $dropdown $GRCh $psm $output1 $output2 $output3 $output4</command> + <command interpreter="python">cravat_submit.py $input $dropdown $GRCh $psm $Variant $Gene $Noncoding $Error</command> <inputs> @@ -16,16 +16,18 @@ <option value="GRCh38">GRCh38/hg38</option> <option value="GRCh37">GRCh37/hg19</option> </param> - <param format="tabular" name="psm" type="data" optional="true" label="Peptide Spectrum Match Report (Optional)"> </param> + <param format="tabular" name="psm" type="data" optional="true" label="ProBED File(Optional)"> </param> </inputs> <outputs> - <data format="cravat" label="CRAVAT: Variant Report" name="output1" /> - <data format="cravat" label="CRAVAT: Gene Level Annotation Report" name="output2" /> - <data format="cravat" label="CRAVAT: Non-coding Variant Report" name="output3" /> - <data format="cravat" label="CRAVAT: Errors" name="output4" /> + <collection name="collection" type="list" label="CRAVAT: ${on_string} using ${dropdown}"> + <data format="cravat" label="CRAVAT: Gene Level Annotation Report" name="Gene" /> + <data format="cravat" label="CRAVAT: Variant Report" name="Variant" /> + <data format="cravat" label="CRAVAT: Non-coding Variant Report" name="Noncoding" /> + <data format="cravat" label="CRAVAT: Errors" name="Error" /> + </collection> </outputs> <tests>