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comparison tandem.xml @ 9:50eb60757ca5

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Update
author Ira Cooke <iracooke@gmail.com>
date Sun, 09 Jun 2013 08:19:31 -0500
parents 16080891c80d
children
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8:16080891c80d 9:50eb60757ca5
1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.1"> 1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.1">
2 2
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.0">galaxy_protk</requirement> 4 <requirement type="package" version="1.2.2">galaxy_protk</requirement>
5 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement> 5 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
6 </requirements> 6 </requirements>
7 7
8 <description>Run an X!Tandem Search</description> 8 <description>Run an X!Tandem Search</description>
9 9
10 <command> 10 <command>
11 #if $database.source_select=="built_in": 11 #if $database.source_select=="built_in":
12 rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.dbkey 12 rvm 1.9.3@protk-1.2.2 do tandem_search.rb -d $database.dbkey
13 #else #rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.fasta_file 13 #else #rvm 1.9.3@protk-1.2.2 do tandem_search.rb -d $database.fasta_file
14 #end if 14 #end if
15 15
16 --var-mods=' 16 --var-mods='
17 $variable_mods 17 $variable_mods
18 #for $custom_variable_mod in $custom_variable_mods: 18 #for $custom_variable_mod in $custom_variable_mods:
119 <param name="fasta_file" value="bsa.fasta"/> 119 <param name="fasta_file" value="bsa.fasta"/>
120 <param name="input_file" value="bsa.mzML"/> 120 <param name="input_file" value="bsa.mzML"/>
121 <param name="variable_mods" value="15.994915@M"/> 121 <param name="variable_mods" value="15.994915@M"/>
122 <param name="fixed_mods" value="57.021464@C"/> 122 <param name="fixed_mods" value="57.021464@C"/>
123 <param name="allow_multi_isotope_search" value="false"/> 123 <param name="allow_multi_isotope_search" value="false"/>
124 <output name="output" file="bsa.pepXML" compare="sim_size" delta="100" /> 124 <output name="output" file="bsa.pepXML" compare="sim_size" delta="600" />
125 </test> 125 </test>
126 </tests> 126 </tests>
127 127
128 128
129 <help> 129 <help>