# HG changeset patch
# User iracooke
# Date 1445388425 14400
# Node ID 0faaab4f192a099f1af010797ad8e69091094942
# Parent 9d6e0ad4d60071981642906c4769a68b6f0dcaed
planemo upload for repository https://github.com/iracooke/protk-galaxytools/tree/master/xtandem commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
diff -r 9d6e0ad4d600 -r 0faaab4f192a repository_dependencies.xml
--- a/repository_dependencies.xml Thu Mar 26 19:53:53 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
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diff -r 9d6e0ad4d600 -r 0faaab4f192a tandem.xml
--- a/tandem.xml Thu Mar 26 19:53:53 2015 -0400
+++ b/tandem.xml Tue Oct 20 20:47:05 2015 -0400
@@ -1,206 +1,180 @@
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+ Run an X!Tandem Search
- iracooke/protk-1.4.1
- protk
-
-
- Run an X!Tandem Search
+ iracooke/protk-1.4.3
+ protk
+
+
+ #if $database.source_select=="built_in":
+ tandem_search.rb -d $database.dbkey
+ #else
+ tandem_search.rb -d $database.fasta_file
+ #end if
-
- #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
+ #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
- '
+ --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
+ --fix-mods='
+ $fixed_mods
+ #for $custom_fix_mod in $custom_fix_mods:
+ ,${custom_fix_mod.custom_mod}
+ #end for
+ '
- --precursor-ion-tol-units=$precursor_tolu
-
- -v $missed_cleavages
+ $input_file -o $output -r
- -f $fragment_ion_tol
-
- -p $precursor_ion_tol
-
- $allow_multi_isotope_search
+ --enzyme=$enzyme
- $acetyl_protein_nterm
-
- $cleavage_semi
-
- $keep_spectra
-
- --threads $threads
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+ --precursor-ion-tol-units=$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 "\${GALAXY_SLOTS:-12}"
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**What it does**
diff -r 9d6e0ad4d600 -r 0faaab4f192a tandem_to_pepxml.xml
--- a/tandem_to_pepxml.xml Thu Mar 26 19:53:53 2015 -0400
+++ b/tandem_to_pepxml.xml Tue Oct 20 20:47:05 2015 -0400
@@ -1,38 +1,33 @@
-
-
- iracooke/protk-1.4.1
- protk
- trans_proteomic_pipeline
+
+ Converts a tandem result file to pepXML
+
+ iracooke/protk-1.4.3
+ protk
+ trans_proteomic_pipeline
+
+ tandem_to_pepxml.rb $input_file -o $output
+
- Converts a tandem result file to pepXML
-
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- tandem_to_pepxml.rb $input_file -o $output
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- Convert X!Tandem results to pepXML
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+ Convert X!Tandem results to pepXML
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diff -r 9d6e0ad4d600 -r 0faaab4f192a tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Tue Oct 20 20:47:05 2015 -0400
@@ -0,0 +1,9 @@
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