# HG changeset patch
# User iracooke
# Date 1402912075 14400
# Node ID 618d74240c7ff7a5c6ec76bcb020f9dda31d23f9
# Parent ffd1d25b8080e04f7e26cf7b65f5e1528095d900
Uploaded
diff -r ffd1d25b8080 -r 618d74240c7f README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Mon Jun 16 05:47:55 2014 -0400
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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 ffd1d25b8080 -r 618d74240c7f README.md
--- a/README.md Mon Jun 16 05:47:38 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 ffd1d25b8080 -r 618d74240c7f repository_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/repository_dependencies.xml Mon Jun 16 05:47:55 2014 -0400
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diff -r ffd1d25b8080 -r 618d74240c7f tandem.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tandem.xml Mon Jun 16 05:47:55 2014 -0400
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+
+
+
+ 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
+
+ -f $fragment_ion_tol
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+ -p $precursor_ion_tol
+
+ $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 ffd1d25b8080 -r 618d74240c7f tandem_to_pepxml.xml
--- a/tandem_to_pepxml.xml Mon Jun 16 05:47:38 2014 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-
-
- 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 ffd1d25b8080 -r 618d74240c7f tool-data/pepxml_databases.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/pepxml_databases.loc.sample Mon Jun 16 05:47:55 2014 -0400
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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 ffd1d25b8080 -r 618d74240c7f tool-data/tandem_mods.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/tandem_mods.loc.sample Mon Jun 16 05:47:55 2014 -0400
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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_
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