Mercurial > repos > iracooke > xtandem

comparison tandem.xml @ 2:5d2228f63b53

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iracooke
date Mon, 04 Mar 2013 01:51:22 -0500
parents 29896659f3ea
children 0c2ee2a55613
comparison
equal deleted inserted replaced
1:b4123e38df43 2:5d2228f63b53
1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.0"> 1 <tool id="proteomics_search_tandem_1" name="X!Tandem 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="4.6.1">trans_proteomic_pipeline</requirement>
6 </requirements>
7
3 <description>Run an X!Tandem Search</description> 8 <description>Run an X!Tandem Search</description>
4 9
5 <command> 10 <command>
6 #if $database.source_select=="built_in": 11 #if $database.source_select=="built_in":
7 tandem_search.rb -d $database.dbkey 12 rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.dbkey
8 #else #tandem_search.rb -d $database.fasta_file 13 #else #rvm 1.9.3@protk-1.1.9 do tandem_search.rb -d $database.fasta_file
9 #end if 14 #end if
10 15
11 --var-mods=' 16 --var-mods='
12 $variable_mods 17 $variable_mods
13 #for $custom_variable_mod in $custom_variable_mods: 18 #for $custom_variable_mod in $custom_variable_mods:
21 ,${custom_fix_mod.custom_mod} 26 ,${custom_fix_mod.custom_mod}
22 #end for 27 #end for
23 ' 28 '
24 29
25 $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol $allow_multi_isotope_search --keep-params-files 30 $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol $allow_multi_isotope_search --keep-params-files
26
27
28 31
29 </command> 32 </command>
30 33
31 <inputs> 34 <inputs>
32 <conditional name="database"> 35 <conditional name="database">
108 111
109 <outputs> 112 <outputs>
110 <data format="raw_pepxml" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/> 113 <data format="raw_pepxml" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/>
111 </outputs> 114 </outputs>
112 115
116 <tests>
117 <test>
118 <param name="source_select" value="input_ref"/>
119 <param name="fasta_file" value="bsa.fasta"/>
120 <param name="input_file" value="bsa.mzML"/>
121 <param name="variable_mods" value="15.994915@M"/>
122 <param name="fixed_mods" value="57.021464@C"/>
123 <param name="allow_multi_isotope_search" value="false"/>
124 <output name="output" file="bsa.pepXML" compare="sim_size" delta="100" />
125 </test>
126 </tests>
127
113 128
114 <help> 129 <help>
115 130
116 **What it does** 131 **What it does**
117 132