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author iracooke
date Thu, 06 Jun 2013 01:33:45 -0400
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1 <tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.1">
2
3 <requirements>
4 <requirement type="package" version="1.2.0">galaxy_protk</requirement>
5 <requirement type="package" version="2.1.9">omssa</requirement>
6 <requirement type="package" version="2.2.27">blast</requirement>
7 </requirements>
8
9
10 <description>Run an OMSSA MS/MS Search</description>
11
12 <command>#if $database.source_select=="built_in":
13 rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.dbkey
14 #else #rvm 1.9.3@protk-1.2.0 do omssa_search.rb -d $database.fasta_file
15 #end if
16
17 --var-mods='
18 $variable_mods
19 '
20
21 --fix-mods='
22 $fixed_mods
23 '
24
25 --searched-ions='
26 $searched_ions
27 '
28
29 $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --num-peaks-for-multi-isotope-search $multi_isotope $use_average_mass $respect_precursor_charges --max-hit-expect $max_hit_expect --intensity-cut-off $intensity_cut_off
30
31 </command>
32
33
34 <inputs>
35 <conditional name="database">
36 <param name="source_select" type="select" label="Database source">
37 <option value="built_in">Built-In</option>
38 <option value="input_ref">Uploaded fasta file</option>
39 </param>
40 <when value="built_in">
41 <param name="dbkey" type="select" format="text" >
42 <label>Database</label>
43 <options from_file="pepxml_databases.loc">
44 <column name="name" index="0" />
45 <column name="value" index="2" />
46 </options>
47 </param>
48 </when>
49 <when value="input_ref">
50 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
51 </when>
52 </conditional>
53
54 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/>
55
56 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
57 clicking to select multiple items">
58 <options from_file="omssa_mods.loc">
59 <column name="name" index="0" />
60 <column name="value" index="2" />
61 </options>
62 </param>
63
64 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
65 clicking to select multiple items">
66 <options from_file="omssa_mods.loc">
67 <column name="name" index="0" />
68 <column name="value" index="2" />
69 </options>
70 </param>
71
72
73 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
74 <label>Missed Cleavages Allowed</label>
75 <option value="0">0</option>
76 <option value="1">1</option>
77 <option value="2">2</option>
78 </param>
79
80 <param name="enzyme" type="select" format="text">
81 <label>Enzyme</label>
82 <option value="0">Trypsin</option>
83 <option value="1">Arg-C</option>
84 <option value="2">CNBr</option>
85 <option value="3">Chymotrypsin (FYWL)</option>
86 <option value="4">Formic Acid</option>
87 <option value="5">Lys-C</option>
88 <option value="6">Lys-C, no P rule</option>
89 <option value="7">Pepsin A</option>
90 <option value="8">Trypsin+CNBr</option>
91 <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option>
92 <option value="10">Trypsin, no P rule</option>
93 <option value="11">Whole protein</option>
94 <option value="12">Asp-N</option>
95 <option value="13">Glu-C</option>
96 <option value="14">Asp-N+Glu-C</option>
97 <option value="15">Top-Down</option>
98 <option value="16">Semi-Tryptic</option>
99 <option value="17">No Enzyme</option>
100 <option value="18">Chymotrypsin, no P rule (FYWL)</option>
101 <option value="19">Asp-N (DE)</option>
102 <option value="20">Glu-C (DE)</option>
103 <option value="21">Lys-N (K)</option>
104 <option value="22">Thermolysin, no P rule</option>
105 <option value="23">Semi-Chymotrypsin (FYWL)</option>
106 <option value="24">Semi-Glu-C</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 <param name="max_hit_expect" help="Expect values less than this are considered to be hits. Use a large value, eg 10000 when results will be processed downstream with Peptide Prophet" type="float" value="1.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he-->
111 <param name="intensity_cut_off" help="Peak intensity cut-off as a fraction of maximum peak intensity" type="float" value="0.0005" min="0" max="1" label="Peak intensity cut-off"/><!-- -ci-->
112
113
114 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
115 <param name="precursor_tolu" type="select" format="text">
116 <label>Precursor Ion Tolerance Units</label>
117 <option value="ppm">ppm</option>
118 <option value="Da">Da</option>
119 </param>
120
121 <param name="use_average_mass" type="boolean" label="Use average precursor masses" help="Match precursor to average mass of the parent ion instead of its monoisotopic mass" truevalue="-a average" falsevalue=""/>
122 <param name="respect_precursor_charges" type="boolean" label="Respect precursor charges" help="Use precursor charge information in input file rather than OMSSA's inferred value" truevalue="--respect-charges" falsevalue=""/>
123
124 <param name="multi_isotope" type="select" format="text" help="Include this many neighbouring peaks when searching for a match to the precursor mass. Only used when doing monoisotopic search">
125 <label>Multi-isotope search.</label>
126 <option value="0">0</option>
127 <option value="1">1</option>
128 <option value="2">2</option>
129 <option value="3">3</option>
130 <option value="4">4</option>
131 </param>
132
133 <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help="">
134 <option selected="true" value="0">a</option>
135 <option selected="true" value="1">b</option>
136 <option value="2">c</option>
137 <option selected="true" value="3">x</option>
138 <option selected="true" value="4">y</option>
139 <option value="5">zdot</option>
140 <option value="10">adot</option>
141 <option value="11">x-CO2</option>
142 <option value="12">adot-CO2</option>
143 </param>
144
145 </inputs>
146
147 <outputs>
148 <data format="raw_pepxml" name="output" metadata_source="input_file" label="omssa_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.pepXML"/>
149 </outputs>
150
151 <help>
152 **What it does**
153
154 Runs an MS/MS database search using the OMSSA search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
155
156 ----
157
158 **Citation**
159
160 If you use this tool please read and cite the paper describing OMSSA.
161
162 Geer L. Y., et al. “Open mass spectrometry search algorithm” *J. Proteome Res.* 3(5), 958-964 (2004).
163
164 </help>
165 </tool>