# HG changeset patch # User simonalpha # Date 1420437343 18000 # Node ID 41ca5c3de8bb546d8207aba2985b358414360e0a # Parent b81c47c81e0acfa7eac0d1f42dc36ad43ce6883e Uploaded diff -r b81c47c81e0a -r 41ca5c3de8bb README --- a/README Fri Jun 13 17:48:00 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -Galaxy wrapper for running the X!Tandem search engine and converting results to pepXML - -Requirements: -This package uses protk and the trans_proteomic_pipeline. These must be installed separately. - -For instructions please see: https://github.com/iracooke/protk/#galaxy-integration \ No newline at end of file diff -r b81c47c81e0a -r 41ca5c3de8bb README.md --- a/README.md Fri Jun 13 17:48:00 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -## What is it? -Galaxy tool definition file and wrapper scripts for the [X!Tandem search engine](http://www.thegpm.org/tandem/index.html). - -## This tool requires that the protk rubygem and X!Tandem itself are installed. - - diff -r b81c47c81e0a -r 41ca5c3de8bb repository_dependencies.xml --- a/repository_dependencies.xml Fri Jun 13 17:48:00 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ - - - - diff -r b81c47c81e0a -r 41ca5c3de8bb tandem.xml --- a/tandem.xml Fri Jun 13 17:48:00 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,204 +0,0 @@ - - - - protk - - - Run an X!Tandem Search - - - #if $database.source_select=="built_in": - tandem_search.rb -d $database.dbkey - #else - tandem_search.rb -d $database.fasta_file - #end if - - #if $tandem_params.source_select=="built_in": - -T $tandem_params.paramskey - #else - -T $tandem_params.params_file - #end if - - - --var-mods=' - $variable_mods - #for $custom_variable_mod in $custom_variable_mods: - ,${custom_variable_mod.custom_mod} - #end for - ' - - --fix-mods=' - $fixed_mods - #for $custom_fix_mod in $custom_fix_mods: - ,${custom_fix_mod.custom_mod} - #end for - ' - - $input_file -o $output -r - - --enzyme=$enzyme - - --precursor-ion-tol-units=$precursor_tolu - - -v $missed_cleavages - - -f $fragment_ion_tol - - -p $precursor_ion_tol - - $allow_multi_isotope_search - - $acetyl_protein_nterm - - $cleavage_semi - - $keep_spectra - - --threads $threads - - - - - - - - - - - - Database - - - - - - - - - - - - - - - - - - - Paramset - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Missed Cleavages Allowed - - - - - - - - - - - - - Enzyme - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Precursor Ion Tolerance Units - - - - - - - - - - - - - - - - -**What it does** - -Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores. - ----- - -**References** - -Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine. - - - - diff -r b81c47c81e0a -r 41ca5c3de8bb tandem_to_pepxml.xml --- a/tandem_to_pepxml.xml Fri Jun 13 17:48:00 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,29 +0,0 @@ - - - protk - trans_proteomic_pipeline - - - Converts a tandem result file to pepXML - -tandem_to_pepxml.rb - $input_file - - -o $output - - - - - - - - - - - - - - Convert X!Tandem results to pepXML - - - diff -r b81c47c81e0a -r 41ca5c3de8bb tool-data/pepxml_databases.loc.sample --- a/tool-data/pepxml_databases.loc.sample Fri Jun 13 17:48:00 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,13 +0,0 @@ -#This file lists the names of protein databases installed locally in protk. -# These are used by omssa and x!tandem as well as the "mascot to pepxml" tool -# In order to combine search results with Interprophet searches must be run against an identical database -# -# Entries should follow the be structured as follows -# Display_name omssa_tandem_dbname dbkey -# -# -Swissprot spall_ spall spall_ -Combined PlasmboDB (falciparum) and Swissprot Human plasmodb_pfalciparum_sphuman_ plasmodb_pfalciparum_sphuman plasmodb_pfalciparum_sphuman_ -Swissprot Human sphuman_ sphuman sphuman_ -Combined Swissprot/TRembl Human sptrhuman_ sptrhuman sptrhuman_ -Swissprot Mouse spmouse_ spmouse spmouse_ diff -r b81c47c81e0a -r 41ca5c3de8bb tool-data/tandem_mods.loc.sample --- a/tool-data/tandem_mods.loc.sample Fri Jun 13 17:48:00 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,6 +0,0 @@ -#This file lists the names of inbuilt chemical modifications accepted by X!Tandem -# -# -Carbamidomethyl C carbamidomethyl_c_ 57.021464@C carbamidomethyl_c_ -Glycocapture-N glycocapture_n_ 0.998@N!{P}[ST] glycocapture_n_ -Oxidation M oxidation_m_ 15.994915@M oxidation_m_ \ No newline at end of file