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planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/omssa/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 20:31:23 -0400
parents 11db804a50b9
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24:11db804a50b9 25:ea9ae5b25ce1
1 <tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.0.1"> 1 <tool id="proteomics_search_omssa_1" name="OMSSA MSMS Search" version="1.1.1">
2 <description>Run an OMSSA MS/MS Search</description>
3 <requirements>
4 <container type="docker">iracooke/protk-1.4.3</container>
5 <requirement type="package" version="1.4.3">protk</requirement>
6 <requirement type="package" version="2.1.9">omssa</requirement>
7 <requirement type="package" version="2.2.29">blast+</requirement>
8 </requirements>
9 <command>omssa_search.rb
2 10
3 <requirements> 11 #if $database.source_select=="built_in":
4 <container type="docker">simonalpha/protk:1.4.0</container> 12 -d $database.dbkey
5 <requirement type="package" version="1.3">protk</requirement> 13 #else
6 <requirement type="package" version="2.1.9">omssa</requirement> 14 -d $database.fasta_file
7 <requirement type="package" version="2.2.29">blast+</requirement> 15 #end if
8 </requirements> 16 --var-mods='
17 $variable_mods
18 '
19
20 --fix-mods='
21 $fixed_mods
22 '
23
24 --searched-ions='
25 $searched_ions
26 '
27
28 $input_file
29 -o $output
30 -r
31
32 --enzyme=$enzyme
33 --precursor-ion-tol-units=$precursor_tolu
34 -v $missed_cleavages
35 -f $fragment_ion_tol
36 -p $precursor_ion_tol
37 --num-peaks-for-multi-isotope-search $multi_isotope
38
39 $use_average_mass
40 $respect_precursor_charges
41
42 --max-hit-expect $max_hit_expect
43 --intensity-cut-off $intensity_cut_off
44
45 </command>
46 <inputs>
47 <conditional name="database">
48 <param name="source_select" type="select" label="Database source">
49 <option value="built_in">Built-In</option>
50 <option selected="true" value="input_ref">Uploaded fasta file</option>
51 </param>
52 <when value="built_in">
53 <param name="dbkey" type="select" format="text" >
54 <label>Database</label>
55 <options from_file="pepxml_databases.loc">
56 <column name="name" index="0" />
57 <column name="value" index="2" />
58 </options>
59 </param>
60 </when>
61 <when value="input_ref">
62 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
63 </when>
64 </conditional>
65 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/>
66 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
67 clicking to select multiple items">
68 <options from_file="omssa_mods.loc">
69 <column name="name" index="0" />
70 <column name="value" index="2" />
71 </options>
72 </param>
73 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications"
74 help="Hold the appropriate key while clicking to select multiple items">
75 <options from_file="omssa_mods.loc">
76 <column name="name" index="0" />
77 <column name="value" index="2" />
78 </options>
79 </param>
80 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
81 <label>Missed Cleavages Allowed</label>
82 <option value="0">0</option>
83 <option value="1">1</option>
84 <option selected="true" value="2">2</option>
85 </param>
86 <param name="enzyme" type="select" format="text">
87 <label>Enzyme</label>
88 <option value="0">Trypsin</option>
89 <option value="1">Arg-C</option>
90 <option value="2">CNBr</option>
91 <option value="3">Chymotrypsin (FYWL)</option>
92 <option value="4">Formic Acid</option>
93 <option value="5">Lys-C</option>
94 <option value="6">Lys-C, no P rule</option>
95 <option value="7">Pepsin A</option>
96 <option value="8">Trypsin+CNBr</option>
97 <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option>
98 <option value="10">Trypsin, no P rule</option>
99 <option value="11">Whole protein</option>
100 <option value="12">Asp-N</option>
101 <option value="13">Glu-C</option>
102 <option value="14">Asp-N+Glu-C</option>
103 <option value="15">Top-Down</option>
104 <option value="16">Semi-Tryptic</option>
105 <option value="17">No Enzyme</option>
106 <option value="18">Chymotrypsin, no P rule (FYWL)</option>
107 <option value="19">Asp-N (DE)</option>
108 <option value="20">Glu-C (DE)</option>
109 <option value="21">Lys-N (K)</option>
110 <option value="22">Thermolysin, no P rule</option>
111 <option value="23">Semi-Chymotrypsin (FYWL)</option>
112 <option value="24">Semi-Glu-C</option>
113 </param>
114
115 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>
116 <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="10000.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he-->
117 <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-->
118
119 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
120 <param name="precursor_tolu" type="select" format="text">
121 <label>Precursor Ion Tolerance Units</label>
122 <option value="ppm">ppm</option>
123 <option value="Da">Da</option>
124 </param>
125
126 <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=""/>
127 <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=""/>
128
129 <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">
130 <label>Multi-isotope search.</label>
131 <option value="0">0</option>
132 <option value="1">1</option>
133 <option value="2">2</option>
134 <option value="3">3</option>
135 <option value="4">4</option>
136 </param>
137
138 <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help="">
139 <option value="0">a</option>
140 <option selected="true" value="1">b</option>
141 <option value="2">c</option>
142 <option value="3">x</option>
143 <option selected="true" value="4">y</option>
144 <option value="5">zdot</option>
145 <option value="10">adot</option>
146 <option value="11">x-CO2</option>
147 <option value="12">adot-CO2</option>
148 </param>
149
150 </inputs>
151 <outputs>
152 <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"/>
153 </outputs>
154 <tests>
155 <!-- Just test that the tool runs and produces vaguely correct output -->
156 <test>
157 <param name="source_select" value="input_ref"/>
158 <param name="fasta_file" value="AASequences.fasta" format="fasta"/>
159 <param name="input_file" value="mr176-BSA100fmole_BA3_01_8168.d.mgf" format="mgf"/>
160 <param name="max_hit_expect" value="1000"/>
161 <param name="precursor_ion_tol" value="1.2"/>
162 <param name="precursor_tolu" value="Da"/>
163 <param name="fix_mods" value="3"/>
164 <param name="variable_mods" value="1"/>
9 165
10 166
11 <description>Run an OMSSA MS/MS Search</description> 167 <output name="output" format="raw_pepxml">
12 168 <assert_contents>
13 <command>omssa_search.rb 169 <has_text text="VLFSQAQVYELERRFK" />
170 </assert_contents>
171 </output>
172 </test>
173 </tests>
14 174
15 #if $database.source_select=="built_in": 175 <help>
16 -d $database.dbkey
17 #else
18 -d $database.fasta_file
19 #end if
20
21 --var-mods='
22 $variable_mods
23 '
24
25 --fix-mods='
26 $fixed_mods
27 '
28
29 --searched-ions='
30 $searched_ions
31 '
32
33 $input_file
34 -o $output
35 -r
36
37 --enzyme=$enzyme
38
39 --precursor-ion-tol-units=$precursor_tolu
40
41 -v $missed_cleavages
42
43 -f $fragment_ion_tol
44
45 -p $precursor_ion_tol
46
47 --num-peaks-for-multi-isotope-search $multi_isotope
48
49 $use_average_mass
50 $respect_precursor_charges
51
52 --max-hit-expect $max_hit_expect
53
54 --intensity-cut-off $intensity_cut_off
55
56 </command>
57
58
59 <inputs>
60 <conditional name="database">
61 <param name="source_select" type="select" label="Database source">
62 <option value="built_in">Built-In</option>
63 <option selected="true" value="input_ref">Uploaded fasta file</option>
64 </param>
65 <when value="built_in">
66 <param name="dbkey" type="select" format="text" >
67 <label>Database</label>
68 <options from_file="pepxml_databases.loc">
69 <column name="name" index="0" />
70 <column name="value" index="2" />
71 </options>
72 </param>
73 </when>
74 <when value="input_ref">
75 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
76 </when>
77 </conditional>
78
79 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="An mgf file with MS/MS data"/>
80
81 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
82 clicking to select multiple items">
83 <options from_file="omssa_mods.loc">
84 <column name="name" index="0" />
85 <column name="value" index="2" />
86 </options>
87 </param>
88
89 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
90 clicking to select multiple items">
91 <options from_file="omssa_mods.loc">
92 <column name="name" index="0" />
93 <column name="value" index="2" />
94 </options>
95 </param>
96
97
98 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
99 <label>Missed Cleavages Allowed</label>
100 <option value="0">0</option>
101 <option value="1">1</option>
102 <option selected="true" value="2">2</option>
103 </param>
104
105 <param name="enzyme" type="select" format="text">
106 <label>Enzyme</label>
107 <option value="0">Trypsin</option>
108 <option value="1">Arg-C</option>
109 <option value="2">CNBr</option>
110 <option value="3">Chymotrypsin (FYWL)</option>
111 <option value="4">Formic Acid</option>
112 <option value="5">Lys-C</option>
113 <option value="6">Lys-C, no P rule</option>
114 <option value="7">Pepsin A</option>
115 <option value="8">Trypsin+CNBr</option>
116 <option value="9">Trypsin+Chymotrypsin (FYWLKR)</option>
117 <option value="10">Trypsin, no P rule</option>
118 <option value="11">Whole protein</option>
119 <option value="12">Asp-N</option>
120 <option value="13">Glu-C</option>
121 <option value="14">Asp-N+Glu-C</option>
122 <option value="15">Top-Down</option>
123 <option value="16">Semi-Tryptic</option>
124 <option value="17">No Enzyme</option>
125 <option value="18">Chymotrypsin, no P rule (FYWL)</option>
126 <option value="19">Asp-N (DE)</option>
127 <option value="20">Glu-C (DE)</option>
128 <option value="21">Lys-N (K)</option>
129 <option value="22">Thermolysin, no P rule</option>
130 <option value="23">Semi-Chymotrypsin (FYWL)</option>
131 <option value="24">Semi-Glu-C</option>
132 </param>
133
134 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.5" min="0" max="10000" label="Fragment ion tolerance"/>
135 <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="10000.0" min="0" max="10000000" label="Maximum Expect value allowed in the hit list"/><!-- -he-->
136 <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-->
137
138
139 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
140 <param name="precursor_tolu" type="select" format="text">
141 <label>Precursor Ion Tolerance Units</label>
142 <option value="ppm">ppm</option>
143 <option value="Da">Da</option>
144 </param>
145
146 <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=""/>
147 <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=""/>
148
149 <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">
150 <label>Multi-isotope search.</label>
151 <option value="0">0</option>
152 <option value="1">1</option>
153 <option value="2">2</option>
154 <option value="3">3</option>
155 <option value="4">4</option>
156 </param>
157
158 <param name="searched_ions" display="checkboxes" type="select" multiple="true" format="text" label="Ions included in search" help="">
159 <option value="0">a</option>
160 <option selected="true" value="1">b</option>
161 <option value="2">c</option>
162 <option value="3">x</option>
163 <option selected="true" value="4">y</option>
164 <option value="5">zdot</option>
165 <option value="10">adot</option>
166 <option value="11">x-CO2</option>
167 <option value="12">adot-CO2</option>
168 </param>
169
170 </inputs>
171
172 <outputs>
173 <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"/>
174 </outputs>
175
176 <help>
177 **What it does** 176 **What it does**
178 177
179 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. 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.
180 179
181 ---- 180 ----
184 183
185 If you use this tool please read and cite the paper describing OMSSA. 184 If you use this tool please read and cite the paper describing OMSSA.
186 185
187 Geer L. Y., et al. “Open mass spectrometry search algorithm” *J. Proteome Res.* 3(5), 958-964 (2004). 186 Geer L. Y., et al. “Open mass spectrometry search algorithm” *J. Proteome Res.* 3(5), 958-964 (2004).
188 187
189 </help> 188 </help>
190 </tool> 189 </tool>