annotate omssa.xml @ 2:418f42b34049 draft

Reuploading
author iracooke
date Mon, 23 Jul 2012 00:20:58 -0400
parents
children 255b5b6ec617
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
418f42b34049 Reuploading
iracooke
parents:
diff changeset
1 <tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.0">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
2 <requirements>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
3 <requirement type="package">protk</requirement>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
4 </requirements>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
5
418f42b34049 Reuploading
iracooke
parents:
diff changeset
6 <description>Run an OMSSA MS/MS Search</description>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
7
418f42b34049 Reuploading
iracooke
parents:
diff changeset
8 <command>#if $database.source_select=="built_in":
418f42b34049 Reuploading
iracooke
parents:
diff changeset
9 omssa_search.rb -d $database.dbkey
418f42b34049 Reuploading
iracooke
parents:
diff changeset
10 #else #omssa_search.rb -d $database.fasta_file
418f42b34049 Reuploading
iracooke
parents:
diff changeset
11 #end if
418f42b34049 Reuploading
iracooke
parents:
diff changeset
12
418f42b34049 Reuploading
iracooke
parents:
diff changeset
13 --var-mods='
418f42b34049 Reuploading
iracooke
parents:
diff changeset
14 $variable_mods
418f42b34049 Reuploading
iracooke
parents:
diff changeset
15 '
418f42b34049 Reuploading
iracooke
parents:
diff changeset
16
418f42b34049 Reuploading
iracooke
parents:
diff changeset
17 --fix-mods='
418f42b34049 Reuploading
iracooke
parents:
diff changeset
18 $fixed_mods
418f42b34049 Reuploading
iracooke
parents:
diff changeset
19 '
418f42b34049 Reuploading
iracooke
parents:
diff changeset
20
418f42b34049 Reuploading
iracooke
parents:
diff changeset
21 --searched-ions='
418f42b34049 Reuploading
iracooke
parents:
diff changeset
22 $searched_ions
418f42b34049 Reuploading
iracooke
parents:
diff changeset
23 '
418f42b34049 Reuploading
iracooke
parents:
diff changeset
24
418f42b34049 Reuploading
iracooke
parents:
diff changeset
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
418f42b34049 Reuploading
iracooke
parents:
diff changeset
26
418f42b34049 Reuploading
iracooke
parents:
diff changeset
27 </command>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
28
418f42b34049 Reuploading
iracooke
parents:
diff changeset
29
418f42b34049 Reuploading
iracooke
parents:
diff changeset
30 <inputs>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
31 <conditional name="database">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
32 <param name="source_select" type="select" label="Database source">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
33 <option value="built_in">Built-In</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
34 <option value="input_ref">Uploaded fasta file</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
35 </param>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
36 <when value="built_in">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
37 <param name="dbkey" type="select" format="text" >
418f42b34049 Reuploading
iracooke
parents:
diff changeset
38 <label>Database</label>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
39 <options from_file="pepxml_databases.loc">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
40 <column name="name" index="0" />
418f42b34049 Reuploading
iracooke
parents:
diff changeset
41 <column name="value" index="2" />
418f42b34049 Reuploading
iracooke
parents:
diff changeset
42 </options>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
43 </param>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
44 </when>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
45 <when value="input_ref">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
46 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
418f42b34049 Reuploading
iracooke
parents:
diff changeset
47 </when>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
48 </conditional>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
49
418f42b34049 Reuploading
iracooke
parents:
diff changeset
50 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
51
418f42b34049 Reuploading
iracooke
parents:
diff changeset
52 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
418f42b34049 Reuploading
iracooke
parents:
diff changeset
53 clicking to select multiple items">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
54 <options from_file="omssa_mods.loc">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
55 <column name="name" index="0" />
418f42b34049 Reuploading
iracooke
parents:
diff changeset
56 <column name="value" index="2" />
418f42b34049 Reuploading
iracooke
parents:
diff changeset
57 </options>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
58 </param>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
59
418f42b34049 Reuploading
iracooke
parents:
diff changeset
60 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
418f42b34049 Reuploading
iracooke
parents:
diff changeset
61 clicking to select multiple items">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
62 <options from_file="omssa_mods.loc">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
63 <column name="name" index="0" />
418f42b34049 Reuploading
iracooke
parents:
diff changeset
64 <column name="value" index="2" />
418f42b34049 Reuploading
iracooke
parents:
diff changeset
65 </options>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
66 </param>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
67
418f42b34049 Reuploading
iracooke
parents:
diff changeset
68
418f42b34049 Reuploading
iracooke
parents:
diff changeset
69 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
70 <label>Missed Cleavages Allowed</label>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
71 <option value="0">0</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
72 <option value="1">1</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
73 <option value="2">2</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
74 </param>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
75
418f42b34049 Reuploading
iracooke
parents:
diff changeset
76 <param name="enzyme" type="select" format="text">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
77 <label>Enzyme</label>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
78 <option value="0">Trypsin</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
79 <option value="1">Arg-C</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
80 <option value="2">CNBr</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
81 <option value="3">Chymotrypsin (FYWL)</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
82 <option value="4">Formic Acid</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
83 <option value="5">Lys-C</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
84 <option value="6">Lys-C, no P rule</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
85 <option value="7">Pepsin A</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
86 <option value="8">Trypsin+CNBr</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
87 <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
88 <option value="10">Trypsin, no P rule</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
89 <option value="11">Whole protein</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
90 <option value="12">Asp-N</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
91 <option value="13">Glu-C</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
92 <option value="14">Asp-N+Glu-C</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
93 <option value="15">Top-Down</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
94 <option value="16">Semi-Tryptic</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
95 <option value="17">No Enzyme</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
96 <option value="18">Chymotrypsin, no P rule (FYWL)</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
97 <option value="19">Asp-N (DE)</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
98 <option value="20">Glu-C (DE)</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
99 <option value="21">Lys-N (K)</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
100 <option value="22">Thermolysin, no P rule</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
101 <option value="23">Semi-Chymotrypsin (FYWL)</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
102 <option value="24">Semi-Glu-C</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
103 </param>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
104
418f42b34049 Reuploading
iracooke
parents:
diff changeset
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"/>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
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-->
418f42b34049 Reuploading
iracooke
parents:
diff changeset
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-->
418f42b34049 Reuploading
iracooke
parents:
diff changeset
108
418f42b34049 Reuploading
iracooke
parents:
diff changeset
109
418f42b34049 Reuploading
iracooke
parents:
diff changeset
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"/>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
111 <param name="precursor_tolu" type="select" format="text">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
112 <label>Precursor Ion Tolerance Units</label>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
113 <option value="ppm">ppm</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
114 <option value="Da">Da</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
115 </param>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
116
418f42b34049 Reuploading
iracooke
parents:
diff changeset
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=""/>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
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=""/>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
119
418f42b34049 Reuploading
iracooke
parents:
diff changeset
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">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
121 <label>Multi-isotope search.</label>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
122 <option value="0">0</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
123 <option value="1">1</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
124 <option value="2">2</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
125 <option value="3">3</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
126 <option value="4">4</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
127 </param>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
128
418f42b34049 Reuploading
iracooke
parents:
diff changeset
129 <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help="">
418f42b34049 Reuploading
iracooke
parents:
diff changeset
130 <option selected="true" value="0">a</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
131 <option selected="true" value="1">b</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
132 <option value="2">c</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
133 <option selected="true" value="3">x</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
134 <option selected="true" value="4">y</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
135 <option value="5">zdot</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
136 <option value="10">adot</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
137 <option value="11">x-CO2</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
138 <option value="12">adot-CO2</option>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
139 </param>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
140
418f42b34049 Reuploading
iracooke
parents:
diff changeset
141 </inputs>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
142
418f42b34049 Reuploading
iracooke
parents:
diff changeset
143 <outputs>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
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"/>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
145 </outputs>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
146
418f42b34049 Reuploading
iracooke
parents:
diff changeset
147 <help>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
148 **What it does**
418f42b34049 Reuploading
iracooke
parents:
diff changeset
149
418f42b34049 Reuploading
iracooke
parents:
diff changeset
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.
418f42b34049 Reuploading
iracooke
parents:
diff changeset
151
418f42b34049 Reuploading
iracooke
parents:
diff changeset
152 ----
418f42b34049 Reuploading
iracooke
parents:
diff changeset
153
418f42b34049 Reuploading
iracooke
parents:
diff changeset
154 **Citation**
418f42b34049 Reuploading
iracooke
parents:
diff changeset
155
418f42b34049 Reuploading
iracooke
parents:
diff changeset
156 If you use this tool please read and cite the paper describing OMSSA.
418f42b34049 Reuploading
iracooke
parents:
diff changeset
157
418f42b34049 Reuploading
iracooke
parents:
diff changeset
158 Geer L. Y., et al. “Open mass spectrometry search algorithm” *J. Proteome Res.* 3(5), 958-964 (2004).
418f42b34049 Reuploading
iracooke
parents:
diff changeset
159
418f42b34049 Reuploading
iracooke
parents:
diff changeset
160 </help>
418f42b34049 Reuploading
iracooke
parents:
diff changeset
161 </tool>