# HG changeset patch # User simonalpha # Date 1420454276 18000 # Node ID b68f292b2904edc3bca1e34864d860200aaf32f4 # Parent e994d6fadcff8d43178b3761c722a8d06e8c77e1 Uploaded diff -r e994d6fadcff -r b68f292b2904 README --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README Mon Jan 05 05:37:56 2015 -0500 @@ -0,0 +1,6 @@ +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 e994d6fadcff -r b68f292b2904 README.md --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.md Mon Jan 05 05:37:56 2015 -0500 @@ -0,0 +1,8 @@ +## 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 e994d6fadcff -r b68f292b2904 interprophet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/interprophet.xml Mon Jan 05 05:37:56 2015 -0500 @@ -0,0 +1,72 @@ + + + + simonalpha/protk:1.4.0 + protk + trans_proteomic_pipeline + + + + Combine Peptide Prophet results from multiple search engines + + interprophet.rb --galaxy + + -o interprophet_output.pep.xml + + $use_nss + + $use_nrs + + $use_nse + + $use_nsi + + $use_nsm + + --p-thresh $p_thresh + + --threads $threads + +#for $pepxml_file in $pepxml_files: + ${pepxml_file} +#end for + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Takes a set of pepXML files (possibly generated using different search engines) and calculates updated identification probabilities for each peptide. The updated probabilities are based on a statistical model that combines evidence from identifications across all of the input files, spectra, modified states and charge states. + +---- + +**Citation** + +If you use this tool please read and cite the paper describing iProphet + +Shteynberg D, et al. “iProphet: Improved statistical validation of peptide identifications in shotgun proteomics.” *Molecular and Cellular Proteomics* 10, M111.007690 (2011). + + + + diff -r e994d6fadcff -r b68f292b2904 peptide_prophet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/peptide_prophet.xml Mon Jan 05 05:37:56 2015 -0500 @@ -0,0 +1,115 @@ + + + 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 + + -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 + + --threads $threads + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**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. + +---- + +**Citation** + +If you use this tool please read and cite the paper describing the statistical model implemented by Peptide Prophet + +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). + + + + + + + + diff -r e994d6fadcff -r b68f292b2904 pepxml_to_table.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pepxml_to_table.xml Mon Jan 05 05:37:56 2015 -0500 @@ -0,0 +1,31 @@ + + + + simonalpha/protk:1.4.0 + protk + + + + + Converts a pepXML file to a tab delimited text file + + + +pepxml_to_table.rb $input_file -o $output $invert_probs + + + + + + + + + + + + + + Convert a pepXML file to Tab delimited text + + + diff -r e994d6fadcff -r b68f292b2904 protein_prophet.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/protein_prophet.xml Mon Jan 05 05:37:56 2015 -0500 @@ -0,0 +1,93 @@ + + + simonalpha/protk:1.4.0 + protk + trans_proteomic_pipeline + + + Calculate Protein Prophet statistics on search results + + + + + protein_prophet.rb + + --galaxy $input_file + + -o protein_prophet_results.prot.xml + + -r + + $iproph + $nooccam + $groupwts + $normprotlen + $logprobs + $confem + $allpeps + $unmapped + $instances + $delude + + --minprob=$minprob + --minindep=$minindep + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +**What it does** + +Given a set of peptide assignments from MS/MS spectra in the form of a pepXML file, this tool estimates probabilities at the protein level. As output, the tool produces a protXML file, which contains proteins along with the estimated probabilities that those proteins were present. Probabilities are estimated using a statistical model based on the number of peptides corresponding to that protein and the confidence that each of those peptides were assigned correctly. It takes account of the fact that peptides may correspond to more than one protein. + +---- + +**Citation** + +If you use this tool please read and cite the paper describing the statistical model implemented by Protein Prophet + +Nesvizhskii A., et al. “A Statistical Model for Identifying Proteins by Tandem Mass Spectrometry” *Anal. Chem.* 75, 4646-4658 (2003). + + + + + diff -r e994d6fadcff -r b68f292b2904 protxml_to_table.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/protxml_to_table.xml Mon Jan 05 05:37:56 2015 -0500 @@ -0,0 +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 + + + + + + + + + + + + + + + + +**What it does** + +Converts a ProtXML file to a tab separated table + + + + diff -r e994d6fadcff -r b68f292b2904 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Mon Jan 05 05:37:56 2015 -0500 @@ -0,0 +1,4 @@ + + + +