# HG changeset patch
# User simonalpha
# Date 1420437379 18000
# Node ID aadf130415087811443817e6620ec0a74e70f0e0
# Parent 41ca5c3de8bb546d8207aba2985b358414360e0a
Uploaded
diff -r 41ca5c3de8bb -r aadf13041508 README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Mon Jan 05 00:56:19 2015 -0500
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+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
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diff -r 41ca5c3de8bb -r aadf13041508 README.md
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.md Mon Jan 05 00:56:19 2015 -0500
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+## 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 41ca5c3de8bb -r aadf13041508 repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Mon Jan 05 00:56:19 2015 -0500
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diff -r 41ca5c3de8bb -r aadf13041508 tandem.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tandem.xml Mon Jan 05 00:56:19 2015 -0500
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+
+
+
+ simonalpha/protk:1.4.0
+ 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 $output -r
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+ --enzyme=$enzyme
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+ --precursor-ion-tol-units=$precursor_tolu
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+ -v $missed_cleavages
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+ -f $fragment_ion_tol
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+ -p $precursor_ion_tol
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+ $allow_multi_isotope_search
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+ $acetyl_protein_nterm
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+ $cleavage_semi
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+ $keep_spectra
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+ --threads $threads
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+**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 41ca5c3de8bb -r aadf13041508 tandem_to_pepxml.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tandem_to_pepxml.xml Mon Jan 05 00:56:19 2015 -0500
@@ -0,0 +1,26 @@
+
+
+ simonalpha/protk:1.4.0
+ protk
+ trans_proteomic_pipeline
+
+
+ Converts a tandem result file to pepXML
+
+
+ tandem_to_pepxml.rb $input_file -o $output
+
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+ Convert X!Tandem results to pepXML
+
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+
diff -r 41ca5c3de8bb -r aadf13041508 tool-data/pepxml_databases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/pepxml_databases.loc.sample Mon Jan 05 00:56:19 2015 -0500
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+#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 41ca5c3de8bb -r aadf13041508 tool-data/tandem_mods.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tandem_mods.loc.sample Mon Jan 05 00:56:19 2015 -0500
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+#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_
+Biotin K biotin_k_ 226.077598@K biotin_k_
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