Mercurial > repos > iracooke > tpp_prophets
diff peptide_prophet.xml @ 15:0746a2ae9e04 draft
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
| author | iracooke |
|---|---|
| date | Tue, 20 Oct 2015 20:45:24 -0400 |
| parents | d90c8bc10a9c |
| children | 1b86e378de37 |
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--- a/peptide_prophet.xml Thu Mar 26 19:55:19 2015 -0400 +++ b/peptide_prophet.xml Tue Oct 20 20:45:24 2015 -0400 @@ -1,73 +1,66 @@ -<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.0"> +<tool id="proteomics_search_peptide_prophet_1" name="Peptide Prophet" version="1.1.1"> + <description>Calculate Peptide Prophet statistics on search results</description> <requirements> - <container type="docker">iracooke/protk-1.4.1</container> - <requirement type="package" version="1.4">protk</requirement> + <container type="docker">iracooke/protk-1.4.3</container> + <requirement type="package" version="1.4.3">protk</requirement> <requirement type="package" version="4.8.0">trans_proteomic_pipeline</requirement> - </requirements> - - <description>Calculate Peptide Prophet statistics on search results</description> - - <command> - peptide_prophet.rb --galaxy $input_file -o peptide_prophet_output.pep.xml - - -r - $glyco - $useicat - $phospho - $usepi - $usert - $accurate_mass - $no_ntt - $no_nmc - $use_gamma - $use_only_expect - $force_fit - $allow_alt_instruments - $maldi - $usedecoys - --decoy-prefix $decoy_prefix_string - -#if $experiment_label - --experiment-label $experiment_label -#end if + </requirements> + <command> + peptide_prophet.rb + --galaxy $input_file + -o peptide_prophet_output.pep.xml + -r + $glyco + $useicat + $phospho + $usepi + $usert + $accurate_mass + $no_ntt + $no_nmc + $use_gamma + $use_only_expect + $force_fit + $allow_alt_instruments + $maldi + $usedecoys + --decoy-prefix $decoy_prefix_string - --p-thresh $p_thresh - - --threads $threads - - </command> - - <inputs> - - <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"/> + #if $experiment_label + --experiment-label $experiment_label + #end if - <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/> - <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/> - <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/> - <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/> - <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/> - <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/> - <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/> - <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/> - <param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/> - <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. - Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/> - <param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/> - <param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/> - <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/> - <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/> - <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/> - <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/> - <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> - <param name="threads" type="integer" value="1" min="0" label="Threads" help="Number of threads to use"/> - - </inputs> - <outputs> - <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/> - </outputs> + --p-thresh $p_thresh + --threads "\${GALAXY_SLOTS:-12}" -<help> + </command> + <inputs> + <param name="input_file" type="data" format="pepxml,raw_pepxml" multiple="false" label="Raw Search Results" help="These files will typically be outputs from omssa or xtandem search tools"/> + + <param name="glyco" type="boolean" label="Expect true positives to have a glycocapture motif" truevalue="--glyco" falsevalue=""/> + <param name="useicat" type="boolean" label="Use icat information" truevalue="--useicat" falsevalue=""/> + <param name="phospho" type="boolean" label="Use phospho information" truevalue="--phospho" falsevalue=""/> + <param name="usepi" type="boolean" label="Use pI information" truevalue="--usepi" falsevalue=""/> + <param name="usert" type="boolean" label="Use hydrophobicity / RT information" truevalue="--usert" falsevalue=""/> + <param name="accurate_mass" type="boolean" label="Use accurate mass binning" truevalue="--accurate-mass" falsevalue=""/> + <param name="no_ntt" type="boolean" label="Don't use NTT model" truevalue="--no-ntt" falsevalue=""/> + <param name="no_nmc" type="boolean" label="Don't use NMC model" truevalue="--no-nmc" falsevalue=""/> + <param name="use_gamma" type="boolean" label="Use Gamma distribution to model the negatives" help="Applies only to X!Tandem results" truevalue="--usegamma" falsevalue=""/> + <param name="use_only_expect" type="boolean" label="Only use Expect Score as the discriminant" help="Applies only to X!Tandem results. + Helpful for data with homologous top hits e.g. phospho or glyco" truevalue="--use-only-expect" falsevalue=""/> + <param name="force_fit" type="boolean" label="Force fitting" help="Bypasses automatic mixture model checks and forces fitting of a mixture model" truevalue="--force-fit" falsevalue=""/> + <param name="allow_alt_instruments" type="boolean" label="Allow multiple instrument types" help="Warning instead of exit with error if instrument types between runs is different" truevalue="--allow-alt-instruments" falsevalue=""/> + <param name="maldi" type="boolean" label="Maldi data" truevalue="-l" falsevalue=""/> + <param name="usedecoys" type="boolean" label="Use decoys to pin down the negative distribution" truevalue="" falsevalue="--no-decoy"/> + <param name="decoy_prefix_string" help="Prefix string for decoy ids" type="text" value="decoy_" label="Decoy Prefix String" size="20"/> + <param name="experiment_label" help="Used to commonly label all spectra from one experiment" type="text" value="" label="Experiment Label" size="20"/> + <param name="p_thresh" help="Peptides scoring less than this value are discarded" type="float" value="0.05" min="0" max="1" label="Probability Threshold"/> + </inputs> + <outputs> + <data format="peptideprophet_pepxml" name="output" metadata_source="input_file" label="peptide_prophet.${input_file.display_name}.pep.xml" from_work_dir="peptide_prophet_output.pep.xml"/> + </outputs> + <help> **What it does** @@ -82,7 +75,7 @@ Keller A., et al. “Empirical Statistical Model to Estimate the Accuracy of Peptide Identifications Made by MS/MS and Database Search” *Anal. Chem.* 74, 5383-5392 (2002). -</help> + </help> <!--PeptideProphet options [following the 'O']: