Mercurial > repos > iracooke > tpp_prophets
comparison protein_prophet.xml @ 14:d90c8bc10a9c draft
Docker support and update for protk 1.4
| author | iracooke |
|---|---|
| date | Thu, 26 Mar 2015 19:55:19 -0400 |
| parents | 4c66453a168e |
| children | 0746a2ae9e04 |
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| 13:b793fe628648 | 14:d90c8bc10a9c |
|---|---|
| 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="1.1.0"> |
| 2 <requirements> | 2 <requirements> |
| 3 <requirement type="package" version="1.3">protk</requirement> | 3 <container type="docker">iracooke/protk-1.4.1</container> |
| 4 <requirement type="package" version="4.6.3">trans_proteomic_pipeline</requirement> | 4 <requirement type="package" version="1.4">protk</requirement> |
| 5 <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> | |
| 5 </requirements> | 6 </requirements> |
| 6 | 7 |
| 7 <description>Calculate Protein Prophet statistics on search results</description> | 8 <description>Calculate Protein Prophet statistics on search results</description> |
| 8 | 9 |
| 9 | 10 |
| 32 --minindep=$minindep | 33 --minindep=$minindep |
| 33 </command> | 34 </command> |
| 34 <inputs> | 35 <inputs> |
| 35 | 36 |
| 36 <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"/> | 37 <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"/> |
| 37 | |
| 38 | 38 |
| 39 <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/> | 39 <param name="iproph" selected="true" type="boolean" label="Inputs are from iProphet" truevalue="--iprophet-input" falsevalue=""/> |
| 40 <param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/> | 40 <param name="nooccam" type="boolean" label="Don't apply Occam's razor" help="When selected no attempt will be made to derive the simplest protein list explaining observed peptides" truevalue="--no-occam" falsevalue=""/> |
| 41 <param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/> | 41 <param name="groupwts" type="boolean" label="Use group weights" help="Check peptide's total weight (rather than actual weight) in the Protein Group against the threshold" truevalue="--group-wts" falsevalue=""/> |
| 42 <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/> | 42 <param name="normprotlen" type="boolean" label="Normalize NSP using Protein Length" truevalue="--norm-protlen" falsevalue=""/> |