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comparison msgfplus_search.xml @ 1:50002ff2c1f3

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Uploaded
author iracooke
date Mon, 04 Mar 2013 20:17:25 -0500
parents 1049de3f4aed
children 0cfe768bbda1
comparison
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0:1049de3f4aed 1:50002ff2c1f3
1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.0"> 1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.0">
2 <requirements><requirement type="package">protkgem</requirement></requirements> 2
3 <requirements>
4 <requirement type="package" version="1.1.9">galaxy_protk</requirement>
5 <requirement type="package" version="20121116">protk_msgfplus</requirement>
6 </requirements>
7
8
3 <description>Run an MSGF+ Search</description> 9 <description>Run an MSGF+ Search</description>
10
11
12
13 <description>Run an X!Tandem Search</description>
4 14
5 <command> 15 <command>
6 #if $database.source_select=="built_in": 16 #if $database.source_select=="built_in":
7 msgfplus_search.rb --galaxy -d $database.dbkey --java-mem 8000M 17 rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.dbkey
8 #else #msgfplus_search.rb -d $database.fasta_file 18 #else #rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.fasta_file
19 #end if
20
21
22 <command>
23 #if $database.source_select=="built_in":
24 rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb --galaxy -d $database.dbkey
25 #else #rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb -d $database.fasta_file
9 #end if 26 #end if
10 27
11 --var-mods=' 28 --var-mods='
12 $variable_mods 29 $variable_mods
13 #for $custom_variable_mod in $custom_variable_mods: 30 #for $custom_variable_mod in $custom_variable_mods: