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comparison omssa.xml @ 6:ac9be1d4885d draft

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author iracooke
date Sat, 14 Jun 2014 18:01:42 -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="1.3">protk</requirement>
5 <requirement type="package" version="2.1.9">omssa</requirement>
6 <requirement type="package" version="2.2.29">blast+</requirement>
7 </requirements>
8
9
10 <description>Run an OMSSA MS/MS Search</description>
11
12 <command>omssa_search.rb
13
14 #if $database.source_select=="built_in":
15 -d $database.dbkey
16 #else
17 -d $database.fasta_file
18 #end if
19
20 --var-mods='
21 $variable_mods
22 '
23
24 --fix-mods='
25 $fixed_mods
26 '
27
28 --searched-ions='
29 $searched_ions
30 '
31
32 $input_file
33 -o $output
34 -r
35
36 --enzyme=$enzyme
37
38 --precursor-ion-tol-units=$precursor_tolu
39
40 -v $missed_cleavages
41
42 -f $fragment_ion_tol
43
44 -p $precursor_ion_tol
45
46 --num-peaks-for-multi-isotope-search $multi_isotope
47
48 $use_average_mass
49 $respect_precursor_charges
50
51 --max-hit-expect $max_hit_expect
52
53 --intensity-cut-off $intensity_cut_off
54
55 </command>
56
57
58 <inputs>
59 <conditional name="database">
60 <param name="source_select" type="select" label="Database source">
61 <option value="built_in">Built-In</option>
62 <option value="input_ref">Uploaded fasta file</option>
63 </param>
64 <when value="built_in">
65 <param name="dbkey" type="select" format="text" >
66 <label>Database</label>
67 <options from_file="pepxml_databases.loc">
68 <column name="name" index="0" />
69 <column name="value" index="2" />
70 </options>
71 </param>
72 </when>
73 <when value="input_ref">
74 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
75 </when>
76 </conditional>
77
78 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/>
79
80 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
81 clicking to select multiple items">
82 <options from_file="omssa_mods.loc">
83 <column name="name" index="0" />
84 <column name="value" index="2" />
85 </options>
86 </param>
87
88 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
89 clicking to select multiple items">
90 <options from_file="omssa_mods.loc">
91 <column name="name" index="0" />
92 <column name="value" index="2" />
93 </options>
94 </param>
95
96
97 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
98 <label>Missed Cleavages Allowed</label>
99 <option value="0">0</option>
100 <option value="1">1</option>
101 <option value="2">2</option>
102 </param>
103
104 <param name="enzyme" type="select" format="text">
105 <label>Enzyme</label>
106 <option value="0">Trypsin</option>
107 <option value="1">Arg-C</option>
108 <option value="2">CNBr</option>
109 <option value="3">Chymotrypsin (FYWL)</option>
110 <option value="4">Formic Acid</option>
111 <option value="5">Lys-C</option>
112 <option value="6">Lys-C, no P rule</option>
113 <option value="7">Pepsin A</option>
114 <option value="8">Trypsin+CNBr</option>
115 <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option>
116 <option value="10">Trypsin, no P rule</option>
117 <option value="11">Whole protein</option>
118 <option value="12">Asp-N</option>
119 <option value="13">Glu-C</option>
120 <option value="14">Asp-N+Glu-C</option>
121 <option value="15">Top-Down</option>
122 <option value="16">Semi-Tryptic</option>
123 <option value="17">No Enzyme</option>
124 <option value="18">Chymotrypsin, no P rule (FYWL)</option>
125 <option value="19">Asp-N (DE)</option>
126 <option value="20">Glu-C (DE)</option>
127 <option value="21">Lys-N (K)</option>
128 <option value="22">Thermolysin, no P rule</option>
129 <option value="23">Semi-Chymotrypsin (FYWL)</option>
130 <option value="24">Semi-Glu-C</option>
131 </param>
132
133 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
134 <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-->
135 <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-->
136
137
138 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
139 <param name="precursor_tolu" type="select" format="text">
140 <label>Precursor Ion Tolerance Units</label>
141 <option value="ppm">ppm</option>
142 <option value="Da">Da</option>
143 </param>
144
145 <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=""/>
146 <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=""/>
147
148 <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">
149 <label>Multi-isotope search.</label>
150 <option value="0">0</option>
151 <option value="1">1</option>
152 <option value="2">2</option>
153 <option value="3">3</option>
154 <option value="4">4</option>
155 </param>
156
157 <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help="">
158 <option selected="true" value="0">a</option>
159 <option selected="true" value="1">b</option>
160 <option value="2">c</option>
161 <option selected="true" value="3">x</option>
162 <option selected="true" value="4">y</option>
163 <option value="5">zdot</option>
164 <option value="10">adot</option>
165 <option value="11">x-CO2</option>
166 <option value="12">adot-CO2</option>
167 </param>
168
169 </inputs>
170
171 <outputs>
172 <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"/>
173 </outputs>
174
175 <help>
176 **What it does**
177
178 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.
179
180 ----
181
182 **Citation**
183
184 If you use this tool please read and cite the paper describing OMSSA.
185
186 Geer L. Y., et al. “Open mass spectrometry search algorithm” *J. Proteome Res.* 3(5), 958-964 (2004).
187
188 </help>
189 </tool>