Mercurial > repos > iracooke > tpp_prophets
comparison protein_prophet.xml @ 5:97f1c89cd831
Uploaded
| author | iracooke |
|---|---|
| date | Mon, 04 Mar 2013 19:09:54 -0500 |
| parents | 25261529840c |
| children | 7005346b534d |
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| 4:a67a5d30bb80 | 5:97f1c89cd831 |
|---|---|
| 1 <tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.0"> | 1 <tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.0"> |
| 2 <requirements> | 2 <requirements> |
| 3 <requirement type="package" version="1.1.9">galaxy_protk</requirement> | 3 <requirement type="package" version="1.1.9">galaxy_protk</requirement> |
| 4 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> | 4 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> |
| 5 </requirements> | 5 </requirements> |
| 6 | 6 |
| 7 <description>Calculate Protein Prophet statistics on search results</description> | 7 <description>Calculate Protein Prophet statistics on search results</description> |
| 8 | 8 |
| 9 | 9 |
| 10 <!-- Note .. the input file is assumed to be the first argument --> | 10 <!-- Note .. the input file is assumed to be the first argument --> |
| 11 <command>protein_prophet.rb --galaxy $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command> | 11 <command>protein_prophet_wrapper.rb --galaxy $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command> |
| 12 <inputs> | 12 <inputs> |
| 13 | 13 |
| 14 <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/> | 14 <param name="input_file" type="data" format="peptideprophet_pepxml,interprophet_pepxml" multiple="false" label="Peptide Prophet Results" help="These files will typically be outputs from peptide prophet or interprophet"/> |
| 15 | 15 |
| 16 | 16 |