Mercurial > repos > iracooke > xtandem
comparison tandem.xml @ 9:50eb60757ca5
Update
author | Ira Cooke <iracooke@gmail.com> |
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date | Sun, 09 Jun 2013 08:19:31 -0500 |
parents | 16080891c80d |
children |
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8:16080891c80d | 9:50eb60757ca5 |
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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> |