Mercurial > repos > iracooke > tpp_prophets
comparison peptide_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_peptide_prophet_1" name="Peptide Prophet" version="1.0.1"> | 1 <tool id="proteomics_search_peptide_prophet_1" name="Peptide 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 Peptide Prophet statistics on search results</description> | 7 <description>Calculate Peptide Prophet statistics on search results</description> |
| 8 | 8 |
| 9 <command interpreter="ruby">peptide_prophet_wrapper.rb ${output} ${input_file} -r $glyco $useicat $phospho $usepi $usert $accurate_mass $no_ntt $no_nmc $use_gamma $use_only_expect $force_fit $allow_alt_instruments $maldi | 9 <command interpreter="bash"> |
| 10 peptide_prophet_wrapper.sh $output $input_file | |
| 11 | |
| 12 -r | |
| 13 $glyco | |
| 14 $useicat | |
| 15 $phospho | |
| 16 $usepi | |
| 17 $usert | |
| 18 $accurate_mass | |
| 19 $no_ntt | |
| 20 $no_nmc | |
| 21 $use_gamma | |
| 22 $use_only_expect | |
| 23 $force_fit | |
| 24 $allow_alt_instruments | |
| 25 $maldi | |
| 26 | |
| 10 </command> | 27 </command> |
| 11 | 28 |
| 12 <inputs> | 29 <inputs> |
| 13 | 30 |
| 14 <param name="input_file" type="data" format="raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/> | 31 <param name="input_file" type="data" format="raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/> |