# HG changeset patch # User iracooke # Date 1445388376 14400 # Node ID 84b47300a4c89077210017d7c2251eca34390eea # Parent b68f292b2904edc3bca1e34864d860200aaf32f4 planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/tpp-prophets/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty diff -r b68f292b2904 -r 84b47300a4c8 README --- a/README Mon Jan 05 05:37:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -This package installs wrapper scripts for Peptide Prophet, iProphet and Protein Prophet - -Requirements: -This package uses protk and the tpp which must be installed separately. - -For instructions please see: https://github.com/iracooke/protk/#galaxy-integration \ No newline at end of file diff -r b68f292b2904 -r 84b47300a4c8 README.md --- a/README.md Mon Jan 05 05:37:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,8 +0,0 @@ -## What is it? -Galaxy tool definition files and wrapper scripts for Peptide and Protein inference tools in the [Trans Proteomic Pipeline](http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP) (Peptide Prophet, iProphet and Protein Prophet). - -## Installation -Install from the main galaxy toolshed at http://toolshed.g2.bx.psu.edu/ - -All the tools depend on command-line scripts and databases available in the [protk ruby gem](https://bitbucket.org/iracooke/protk). - diff -r b68f292b2904 -r 84b47300a4c8 README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Tue Oct 20 20:46:16 2015 -0400 @@ -0,0 +1,37 @@ +TPP Prophets +============ + +Galaxy wrappers for Peptide Prophet, iProphet and Protein Prophet + +Requirements +------------ + +This package uses protk_ and the trans_proteomic_pipeline_ which need to be present in order for the tool to work. + +.. _protk: https://github.com/iracooke/protk +.. _trans_proteomic_pipeline: http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP + +There are two ways you can satify these dependencies (choose one): + +1. **Manual Install:** Details on how to install protk_ and the trans_proteomic_pipeline_ manually are available here_. + +2. **Use Docker:** These tools are designed to run inside a docker_ container. If your galaxy supports `running tools within a docker container`__ you don't need to worry about dependencies. Simply install and things should just work. The docker container itself is versioned and new versions of this tool will automatically download an update to the container if needed. + +.. _docker: https://www.docker.com/ +.. _here: https://github.com/iracooke/protk/#galaxy-integration +.. _container: https://wiki.galaxyproject.org/Admin/Tools/Docker +__ container_ + + +Further Info +------------ + +The source code for this tool and other protk galaxy tools is on github_. Please visit the github page to contribute to the project or to `report an issue`__ + +.. _github: https://github.com/iracooke/protk-galaxytools +.. _issue: https://github.com/iracooke/protk-galaxytools/issues +__ issue_ + +Please visit the TPP__ website for details of the various Prophet tools + +__ trans_proteomic_pipeline_ diff -r b68f292b2904 -r 84b47300a4c8 interprophet.xml --- a/interprophet.xml Mon Jan 05 05:37:56 2015 -0500 +++ b/interprophet.xml Tue Oct 20 20:46:16 2015 -0400 @@ -1,59 +1,71 @@ - - - - simonalpha/protk:1.4.0 - protk - trans_proteomic_pipeline - - - - Combine Peptide Prophet results from multiple search engines - - interprophet.rb --galaxy + + Combine Peptide Prophet results from multiple search engines + + iracooke/protk-1.4.3 + protk + trans_proteomic_pipeline + + + - - - - - +]]> + + - - - - - - - + + + + + + + + + + + + + + + - - - - - - + - + + + + + + + + + + + + **What it does** @@ -67,6 +79,5 @@ Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011). - - + diff -r b68f292b2904 -r 84b47300a4c8 peptide_prophet.xml --- a/peptide_prophet.xml Mon Jan 05 05:37:56 2015 -0500 +++ b/peptide_prophet.xml Tue Oct 20 20:46:16 2015 -0400 @@ -1,76 +1,70 @@ - + + Calculate Peptide Prophet statistics on search results - simonalpha/protk:1.4.0 - protk - trans_proteomic_pipeline - - - Calculate Peptide Prophet statistics on search results - - - peptide_prophet.rb --galaxy $input_file -o peptide_prophet_output.pep.xml + iracooke/protk-1.4.3 + protk + trans_proteomic_pipeline + + + 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 - -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 - - --p-thresh $p_thresh + #if $experiment_label + --experiment-label $experiment_label + #end if - --threads $threads + --p-thresh $p_thresh + --threads "\${GALAXY_SLOTS:-12}" - - - - + + + - - - - - - - - - - - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + **What it does** -Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments. From a practical perspective it estimates the probability that each peptide assignment is correct (providing probabilities as outputs), given raw scores (possibly on some arbitrary scale) as inputs. +Given raw search engine scores as inputs this tool estimates the accuracy of peptide assignments. ---- @@ -81,7 +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). - + -pepxml_to_table.rb $input_file -o $output $invert_probs - - - - - - - - - - - - + + Converts a pepXML file to a tab delimited text file + + iracooke/protk-1.4.3 + protk + + + pepxml_to_table.rb $input_file -o $output $invert_probs + + + + + + + + + + + + + + + + + + - Convert a pepXML file to Tab delimited text + Convert a pepXML file to Tab delimited text - diff -r b68f292b2904 -r 84b47300a4c8 protein_prophet.xml --- a/protein_prophet.xml Mon Jan 05 05:37:56 2015 -0500 +++ b/protein_prophet.xml Tue Oct 20 20:46:16 2015 -0400 @@ -1,79 +1,73 @@ - - - simonalpha/protk:1.4.0 - protk - trans_proteomic_pipeline - - - Calculate Protein Prophet statistics on search results - + + Calculate Protein Prophet statistics on search results + + iracooke/protk-1.4.3 + protk + trans_proteomic_pipeline + - - - protein_prophet.rb - - --galaxy $input_file - - -o protein_prophet_results.prot.xml - - -r + + protein_prophet.rb + --galaxy + + #for $input_file in $input_files: + ${input_file} + #end for + + -o protein_prophet_results.prot.xml + -r - $iproph - $nooccam - $groupwts - $normprotlen - $logprobs - $confem - $allpeps - $unmapped - $instances - $delude - - --minprob=$minprob - --minindep=$minindep - - - - + $iproph + $nooccam + $groupwts + $normprotlen + $logprobs + $confem + $allpeps + $unmapped + $instances + $delude + --minprob=$minprob + --minindep=$minindep + + + - - - - - - - - - - + + + + + + + + + + - - - - - - - + + + + + + - + **What it does** @@ -88,6 +82,5 @@ Nesvizhskii A., et al. “A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry” *Anal. Chem.* 75, 4646-4658 (2003). - - + diff -r b68f292b2904 -r 84b47300a4c8 protxml_to_table.xml --- a/protxml_to_table.xml Mon Jan 05 05:37:56 2015 -0500 +++ b/protxml_to_table.xml Tue Oct 20 20:46:16 2015 -0400 @@ -1,37 +1,37 @@ - - - simonalpha/protk:1.4.0 - protk - - - Converts a ProtXML file to a table - - - protxml_to_table.rb - $invert_probs - - $input_file - -o $output - - - - - - - - - - - - - - - - + + Converts a ProtXML file to a table + + iracooke/protk-1.4.3 + protk + + + protxml_to_table.rb + $invert_probs + $input_file + -o $output + + + + + + + + + + + + + + + + + + + + **What it does** Converts a ProtXML file to a tab separated table - - + diff -r b68f292b2904 -r 84b47300a4c8 repository_dependencies.xml --- a/repository_dependencies.xml Mon Jan 05 05:37:56 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - diff -r b68f292b2904 -r 84b47300a4c8 test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem.pep.xml Tue Oct 20 20:46:16 2015 -0400 @@ -0,0 +1,1651 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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