# HG changeset patch # User iracooke # Date 1427414119 14400 # Node ID d90c8bc10a9cc73ec6b6c0e2e454a153fe981391 # Parent b793fe6286481ca2c772f4625b745d04cc7cb9d1 Docker support and update for protk 1.4 diff -r b793fe628648 -r d90c8bc10a9c README.md --- a/README.md Tue Jul 01 11:16:41 2014 -0400 +++ /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 b793fe628648 -r d90c8bc10a9c README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Thu Mar 26 19:55:19 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 b793fe628648 -r d90c8bc10a9c interprophet.xml --- a/interprophet.xml Tue Jul 01 11:16:41 2014 -0400 +++ b/interprophet.xml Thu Mar 26 19:55:19 2015 -0400 @@ -1,8 +1,9 @@ - + - protk - trans_proteomic_pipeline + iracooke/protk-1.4.1 + protk + trans_proteomic_pipeline @@ -22,35 +23,34 @@ $use_nsm - --minprob $minprob + --p-thresh $p_thresh + + --threads $threads - ## Inputs. - ${first_input} - #for $input_file in $input_files: - ${input_file.additional_input} - #end for +#for $pepxml_file in $pepxml_files: + ${pepxml_file} +#end for + - - - - - + + + + + + + - - - - - - - + + + - + diff -r b793fe628648 -r d90c8bc10a9c peptide_prophet.xml --- a/peptide_prophet.xml Tue Jul 01 11:16:41 2014 -0400 +++ b/peptide_prophet.xml Thu Mar 26 19:55:19 2015 -0400 @@ -1,7 +1,8 @@ - + - protk - trans_proteomic_pipeline + iracooke/protk-1.4.1 + protk + trans_proteomic_pipeline Calculate Peptide Prophet statistics on search results @@ -23,6 +24,16 @@ $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 + + --threads $threads @@ -44,18 +55,23 @@ - + + + + + + **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. ---- diff -r b793fe628648 -r d90c8bc10a9c pepxml_to_table.xml --- a/pepxml_to_table.xml Tue Jul 01 11:16:41 2014 -0400 +++ b/pepxml_to_table.xml Thu Mar 26 19:55:19 2015 -0400 @@ -1,7 +1,8 @@ - + - protk + iracooke/protk-1.4.1 + protk @@ -10,18 +11,33 @@ -pepxml_to_table.rb $input_file -o $output +pepxml_to_table.rb $input_file -o $output $invert_probs + + + + + + + + + + + + + + + Convert a pepXML file to Tab delimited text diff -r b793fe628648 -r d90c8bc10a9c protein_prophet.xml --- a/protein_prophet.xml Tue Jul 01 11:16:41 2014 -0400 +++ b/protein_prophet.xml Thu Mar 26 19:55:19 2015 -0400 @@ -1,7 +1,8 @@ - + - protk - trans_proteomic_pipeline + iracooke/protk-1.4.1 + protk + trans_proteomic_pipeline Calculate Protein Prophet statistics on search results @@ -35,7 +36,6 @@ - diff -r b793fe628648 -r d90c8bc10a9c protxml_to_table.xml --- a/protxml_to_table.xml Tue Jul 01 11:16:41 2014 -0400 +++ b/protxml_to_table.xml Thu Mar 26 19:55:19 2015 -0400 @@ -1,12 +1,14 @@ - + - protk + iracooke/protk-1.4.1 + protk Converts a ProtXML file to a table protxml_to_table.rb + $invert_probs $input_file -o $output @@ -15,7 +17,7 @@ - + @@ -23,6 +25,18 @@ + + + + + + + + + + + + diff -r b793fe628648 -r d90c8bc10a9c repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Thu Mar 26 19:55:19 2015 -0400 @@ -0,0 +1,4 @@ + + + + diff -r b793fe628648 -r d90c8bc10a9c 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 Thu Mar 26 19:55:19 2015 -0400 @@ -0,0 +1,1651 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff -r b793fe628648 -r d90c8bc10a9c test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/mr176-BSA100fmole_BA3_01_8168.d_tandem_pproph_protproph.prot.xml Thu Mar 26 19:55:19 2015 -0400 @@ -0,0 +1,262 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +