Mercurial > repos > iracooke > tpp_prophets
comparison protein_prophet.xml @ 8:d19a95abf2e4
Update
| author | Ira Cooke <iracooke@gmail.com> |
|---|---|
| date | Sun, 09 Jun 2013 08:19:01 -0500 |
| parents | 3f0cb90824f1 |
| children |
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| 7:3f0cb90824f1 | 8:d19a95abf2e4 |
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| 1 <tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.1"> | 1 <tool id="proteomics_search_protein_prophet_1" name="Protein Prophet" version="1.0.1"> |
| 2 <requirements> | 2 <requirements> |
| 3 <requirement type="package" version="1.2.0">galaxy_protk</requirement> | 3 <requirement type="package" version="1.2.2">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 interpreter="ruby">protein_prophet_wrapper.rb --galaxy $input_file -r $iproph $nooccam $groupwts $normprotlen $logprobs $confem $allpeps $unmapped $instances $delude --minprob=$minprob --minindep=$minindep </command> | 11 <command interpreter="bash"> |
| 12 protein_prophet_wrapper.sh | |
| 13 | |
| 14 --galaxy $input_file | |
| 15 | |
| 16 -r | |
| 17 | |
| 18 $iproph | |
| 19 $nooccam | |
| 20 $groupwts | |
| 21 $normprotlen | |
| 22 $logprobs | |
| 23 $confem | |
| 24 $allpeps | |
| 25 $unmapped | |
| 26 $instances | |
| 27 $delude | |
| 28 | |
| 29 --minprob=$minprob | |
| 30 --minindep=$minindep | |
| 31 </command> | |
| 12 <inputs> | 32 <inputs> |
| 13 | 33 |
| 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"/> | 34 <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 | 35 |
| 16 | 36 |