# HG changeset patch
# User iracooke
# Date 1445387452 14400
# Node ID 4294476e3f831d99b4478a601aaeb2436efe7452
# Parent 51f6c6446e69e59ed58145f7c5b5bc6f50cb0ba9
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
diff -r 51f6c6446e69 -r 4294476e3f83 omssa.xml
--- a/omssa.xml Thu Mar 26 20:04:12 2015 -0400
+++ b/omssa.xml Tue Oct 20 20:30:52 2015 -0400
@@ -1,184 +1,162 @@
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- iracooke/protk-1.4.1
- protk
- omssa
- blast+
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- Run an OMSSA MS/MS Search
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- omssa_search.rb
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+ Run an OMSSA MS/MS Search
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+ iracooke/protk-1.4.3
+ protk
+ omssa
+ blast+
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+ omssa_search.rb
- #if $database.source_select=="built_in":
- -d $database.dbkey
- #else
- -d $database.fasta_file
- #end if
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- --var-mods='
- $variable_mods
- '
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- --fix-mods='
- $fixed_mods
- '
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- --searched-ions='
- $searched_ions
- '
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- $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
+ #if $database.source_select=="built_in":
+ -d $database.dbkey
+ #else
+ -d $database.fasta_file
+ #end if
+ --var-mods='
+ $variable_mods
+ '
- -p $precursor_ion_tol
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- --num-peaks-for-multi-isotope-search $multi_isotope
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- $use_average_mass
- $respect_precursor_charges
+ --fix-mods='
+ $fixed_mods
+ '
- --max-hit-expect $max_hit_expect
+ --searched-ions='
+ $searched_ions
+ '
- --intensity-cut-off $intensity_cut_off
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+ $input_file
+ -o $output
+ -r
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+ --enzyme=$enzyme
+ --precursor-ion-tol-units=$precursor_tolu
+ -v $missed_cleavages
+ -f $fragment_ion_tol
+ -p $precursor_ion_tol
+ --num-peaks-for-multi-isotope-search $multi_isotope
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+ $use_average_mass
+ $respect_precursor_charges
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+ --max-hit-expect $max_hit_expect
+ --intensity-cut-off $intensity_cut_off
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@@ -186,15 +164,15 @@
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**What it does**
Runs an MS/MS database search using the OMSSA search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
@@ -207,5 +185,5 @@
Geer L. Y., et al. “Open mass spectrometry search algorithm” *J. Proteome Res.* 3(5), 958-964 (2004).
-
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diff -r 51f6c6446e69 -r 4294476e3f83 repository_dependencies.xml
--- a/repository_dependencies.xml Thu Mar 26 20:04:12 2015 -0400
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
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diff -r 51f6c6446e69 -r 4294476e3f83 tool_dependencies.xml
--- a/tool_dependencies.xml Thu Mar 26 20:04:12 2015 -0400
+++ b/tool_dependencies.xml Tue Oct 20 20:30:52 2015 -0400
@@ -1,8 +1,12 @@
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