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comparison msgfplus_search.xml @ 2:0d21fdb9c999

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author iracooke
date Mon, 04 Mar 2013 20:48:04 -0500
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1:528bcbb94199 2:0d21fdb9c999
1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.0">
2
3 <requirements>
4 <requirement type="package" version="1.1.9">galaxy_protk</requirement>
5 <requirement type="package" version="20121116">msgfplus</requirement>
6 <package name="proteowizard" version="3_0_4388">
7 </requirements>
8
9
10 <description>Run an MSGF+ Search</description>
11
12 <command>
13 #if $database.source_select=="built_in":
14 rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb --galaxy -d $database.dbkey
15 #else #rvm 1.9.3@protk-1.1.9 do msgfplus_search.rb -d $database.fasta_file
16 #end if
17
18 --var-mods='
19 $variable_mods
20 #for $custom_variable_mod in $custom_variable_mods:
21 ,${custom_variable_mod.custom_mod}
22 #end for
23 '
24
25 --fix-mods='
26 $fixed_mods
27 #for $custom_fix_mod in $custom_fix_mods:
28 ,${custom_fix_mod.custom_mod}
29 #end for
30 '
31
32 $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --instrument=$instrument
33
34
35
36 </command>
37
38 <inputs>
39 <conditional name="database">
40 <param name="source_select" type="select" label="Database source">
41 <option value="built_in">Built-In</option>
42 <option value="input_ref">Your Upload File</option>
43 </param>
44 <when value="built_in">
45 <param name="dbkey" type="select" format="text" >
46 <label>Database</label>
47 <options from_file="pepxml_databases.loc">
48 <column name="name" index="0" />
49 <column name="value" index="2" />
50 </options>
51 </param>
52 </when>
53 <when value="input_ref">
54 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
55 </when>
56 </conditional>
57
58 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
59
60
61 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
62 clicking to select multiple items">
63 <options from_file="msgfplus_mods.loc">
64 <column name="name" index="0" />
65 <column name="value" index="2" />
66 </options>
67 </param>
68
69 <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
70 <param name="custom_mod" type="text">
71 </param>
72 </repeat>
73
74
75 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
76 clicking to select multiple items">
77 <options from_file="msgfplus_mods.loc">
78 <column name="name" index="0" />
79 <column name="value" index="2" />
80 </options>
81 </param>
82
83 <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
84 <param name="custom_mod" type="text">
85 </param>
86 </repeat>
87
88
89
90 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
91 <label>Missed Cleavages Allowed</label>
92 <option value="0">0</option>
93 <option value="1">1</option>
94 <option value="2">2</option>
95 </param>
96
97 <param name="enzyme" type="select" format="text">
98 <label>Enzyme</label>
99 <option value="Trypsin">Trypsin</option>
100 </param>
101
102 <param name="instrument" type="select" format="text">
103 <label>Instrument Type</label>
104 <option value="2">TOF</option>
105 <option value="0">Low-res LCQ/LTQ</option>
106 <option value="1">High-res LTQ</option>
107 </param>
108
109 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
110
111 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
112 <param name="precursor_tolu" type="select" format="text">
113 <label>Precursor Ion Tolerance Units</label>
114 <option value="ppm">ppm</option>
115 <option value="Da">Da</option>
116 </param>
117
118 </inputs>
119
120
121 <outputs>
122 <data format="raw_pepxml" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/>
123 </outputs>
124
125
126 <help>
127
128 **What it does**
129
130 Runs an MS/MS database search using the MSGFPlus search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
131
132 ----
133
134 **References**
135
136 Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm
137
138 </help>
139
140 </tool>