# HG changeset patch
# User iracooke
# Date 1402917429 14400
# Node ID 4c66453a168e74ac4e61edadc9baa0fc25606c7d
# Parent 8512f117b10b4606cd6c8054a7a2943bf37fd4ad
Uploaded
diff -r 8512f117b10b -r 4c66453a168e README
--- a/README Sat Jun 14 18:26:00 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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-Requirements:
-This package uses protk, msgfplus and proteowizard, which must be installed separately.
-
-For instructions please see: https://github.com/iracooke/protk/#galaxy-integration
\ No newline at end of file
diff -r 8512f117b10b -r 4c66453a168e README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Mon Jun 16 07:17:09 2014 -0400
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+## 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 8512f117b10b -r 4c66453a168e interprophet.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/interprophet.xml Mon Jun 16 07:17:09 2014 -0400
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+
+
+
+ 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
+
+ --minprob $minprob
+
+ ## Inputs.
+ ${first_input}
+ #for $input_file in $input_files:
+ ${input_file.additional_input}
+ #end for
+
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+**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).
+
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+
diff -r 8512f117b10b -r 4c66453a168e peptide_prophet.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/peptide_prophet.xml Mon Jun 16 07:17:09 2014 -0400
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+
+
+ 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
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+**What it does**
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+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).
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diff -r 8512f117b10b -r 4c66453a168e pepxml_to_table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/pepxml_to_table.xml Mon Jun 16 07:17:09 2014 -0400
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+
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+ protk
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+ Converts a pepXML file to a tab delimited text file
+
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+pepxml_to_table.rb $input_file -o $output
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+ Convert a pepXML file to Tab delimited text
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diff -r 8512f117b10b -r 4c66453a168e protein_prophet.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_prophet.xml Mon Jun 16 07:17:09 2014 -0400
@@ -0,0 +1,93 @@
+
+
+ protk
+ trans_proteomic_pipeline
+
+
+ Calculate Protein Prophet statistics on search results
+
+
+
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+ 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
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+**What it does**
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+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).
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diff -r 8512f117b10b -r 4c66453a168e protxml_to_table.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/protxml_to_table.xml Mon Jun 16 07:17:09 2014 -0400
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+
+
+ protk
+
+
+ Converts a ProtXML file to a table
+
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+ protxml_to_table.rb
+
+ $input_file
+ -o $output
+
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+**What it does**
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+Converts a ProtXML file to a tab separated table
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diff -r 8512f117b10b -r 4c66453a168e repository_dependencies.xml
--- a/repository_dependencies.xml Sat Jun 14 18:26:00 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
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