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comparison omssa.xml @ 2:418f42b34049 draft

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Reuploading
author iracooke
date Mon, 23 Jul 2012 00:20:58 -0400
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1:deaedec14cc8 2:418f42b34049
1 <tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.0">
2 <requirements>
3 <requirement type="package">protk</requirement>
4 </requirements>
5
6 <description>Run an OMSSA MS/MS Search</description>
7
8 <command>#if $database.source_select=="built_in":
9 omssa_search.rb -d $database.dbkey
10 #else #omssa_search.rb -d $database.fasta_file
11 #end if
12
13 --var-mods='
14 $variable_mods
15 '
16
17 --fix-mods='
18 $fixed_mods
19 '
20
21 --searched-ions='
22 $searched_ions
23 '
24
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 --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
26
27 </command>
28
29
30 <inputs>
31 <conditional name="database">
32 <param name="source_select" type="select" label="Database source">
33 <option value="built_in">Built-In</option>
34 <option value="input_ref">Uploaded fasta file</option>
35 </param>
36 <when value="built_in">
37 <param name="dbkey" type="select" format="text" >
38 <label>Database</label>
39 <options from_file="pepxml_databases.loc">
40 <column name="name" index="0" />
41 <column name="value" index="2" />
42 </options>
43 </param>
44 </when>
45 <when value="input_ref">
46 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
47 </when>
48 </conditional>
49
50 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/>
51
52 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
53 clicking to select multiple items">
54 <options from_file="omssa_mods.loc">
55 <column name="name" index="0" />
56 <column name="value" index="2" />
57 </options>
58 </param>
59
60 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
61 clicking to select multiple items">
62 <options from_file="omssa_mods.loc">
63 <column name="name" index="0" />
64 <column name="value" index="2" />
65 </options>
66 </param>
67
68
69 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
70 <label>Missed Cleavages Allowed</label>
71 <option value="0">0</option>
72 <option value="1">1</option>
73 <option value="2">2</option>
74 </param>
75
76 <param name="enzyme" type="select" format="text">
77 <label>Enzyme</label>
78 <option value="0">Trypsin</option>
79 <option value="1">Arg-C</option>
80 <option value="2">CNBr</option>
81 <option value="3">Chymotrypsin (FYWL)</option>
82 <option value="4">Formic Acid</option>
83 <option value="5">Lys-C</option>
84 <option value="6">Lys-C, no P rule</option>
85 <option value="7">Pepsin A</option>
86 <option value="8">Trypsin+CNBr</option>
87 <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option>
88 <option value="10">Trypsin, no P rule</option>
89 <option value="11">Whole protein</option>
90 <option value="12">Asp-N</option>
91 <option value="13">Glu-C</option>
92 <option value="14">Asp-N+Glu-C</option>
93 <option value="15">Top-Down</option>
94 <option value="16">Semi-Tryptic</option>
95 <option value="17">No Enzyme</option>
96 <option value="18">Chymotrypsin, no P rule (FYWL)</option>
97 <option value="19">Asp-N (DE)</option>
98 <option value="20">Glu-C (DE)</option>
99 <option value="21">Lys-N (K)</option>
100 <option value="22">Thermolysin, no P rule</option>
101 <option value="23">Semi-Chymotrypsin (FYWL)</option>
102 <option value="24">Semi-Glu-C</option>
103 </param>
104
105 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
106 <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-->
107 <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-->
108
109
110 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
111 <param name="precursor_tolu" type="select" format="text">
112 <label>Precursor Ion Tolerance Units</label>
113 <option value="ppm">ppm</option>
114 <option value="Da">Da</option>
115 </param>
116
117 <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=""/>
118 <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=""/>
119
120 <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">
121 <label>Multi-isotope search.</label>
122 <option value="0">0</option>
123 <option value="1">1</option>
124 <option value="2">2</option>
125 <option value="3">3</option>
126 <option value="4">4</option>
127 </param>
128
129 <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help="">
130 <option selected="true" value="0">a</option>
131 <option selected="true" value="1">b</option>
132 <option value="2">c</option>
133 <option selected="true" value="3">x</option>
134 <option selected="true" value="4">y</option>
135 <option value="5">zdot</option>
136 <option value="10">adot</option>
137 <option value="11">x-CO2</option>
138 <option value="12">adot-CO2</option>
139 </param>
140
141 </inputs>
142
143 <outputs>
144 <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"/>
145 </outputs>
146
147 <help>
148 **What it does**
149
150 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.
151
152 ----
153
154 **Citation**
155
156 If you use this tool please read and cite the paper describing OMSSA.
157
158 Geer L. Y., et al. “Open mass spectrometry search algorithm” *J. Proteome Res.* 3(5), 958-964 (2004).
159
160 </help>
161 </tool>