|
7
|
1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.1">
|
|
1
|
2
|
|
|
3 <requirements>
|
|
8
|
4 <requirement type="package" version="1.2.2">galaxy_protk</requirement>
|
|
4
|
5 <requirement type="package" version="20130227">msgfplus</requirement>
|
|
|
6 <requirement type="package" version="3_0_4388">proteowizard</requirement>
|
|
1
|
7 </requirements>
|
|
|
8
|
|
|
9
|
|
0
|
10 <description>Run an MSGF+ Search</description>
|
|
|
11
|
|
1
|
12 <command>
|
|
8
|
13 rvm 1.9.3@protk-1.2.2 do msgfplus_search.rb
|
|
1
|
14 #if $database.source_select=="built_in":
|
|
8
|
15 --galaxy -d $database.dbkey
|
|
|
16 #else
|
|
|
17 --galaxy -d $database.fasta_file
|
|
0
|
18 #end if
|
|
|
19
|
|
|
20 --var-mods='
|
|
|
21 $variable_mods
|
|
|
22 #for $custom_variable_mod in $custom_variable_mods:
|
|
|
23 ,${custom_variable_mod.custom_mod}
|
|
|
24 #end for
|
|
|
25 '
|
|
|
26
|
|
|
27 --fix-mods='
|
|
|
28 $fixed_mods
|
|
|
29 #for $custom_fix_mod in $custom_fix_mods:
|
|
|
30 ,${custom_fix_mod.custom_mod}
|
|
|
31 #end for
|
|
|
32 '
|
|
|
33
|
|
8
|
34 $input_file
|
|
|
35
|
|
|
36 -o $output
|
|
|
37
|
|
|
38 -r
|
|
|
39
|
|
|
40 --enzyme=$enzyme
|
|
|
41
|
|
|
42 --precursor-ion-tol-units=$precursor_tolu
|
|
|
43
|
|
|
44 -v $missed_cleavages
|
|
|
45
|
|
|
46 -f $fragment_ion_tol
|
|
|
47
|
|
|
48 -p $precursor_ion_tol
|
|
|
49
|
|
|
50 --instrument=$instrument
|
|
0
|
51
|
|
8
|
52 --isotope-error-range=$isotope_error_range
|
|
|
53
|
|
|
54 --fragment-method=$fragment_method
|
|
|
55
|
|
|
56 --protocol=$protocol
|
|
|
57
|
|
|
58 --min-pep-len=$min_pep_len
|
|
|
59 --max-pep-len=$max_pep_len
|
|
|
60 --max-pep-charge=$max_pep_charge
|
|
|
61 --min-pep-charge=$min_pep_charge
|
|
|
62 --num-reported-matches=$num_reported_matches
|
|
|
63
|
|
|
64 --java-mem=$java_mem
|
|
|
65
|
|
|
66 #if $pepxml_output_use
|
|
|
67
|
|
|
68 #else
|
|
|
69 --no-pepxml
|
|
|
70 #end if
|
|
|
71
|
|
0
|
72 </command>
|
|
|
73
|
|
|
74 <inputs>
|
|
|
75 <conditional name="database">
|
|
|
76 <param name="source_select" type="select" label="Database source">
|
|
|
77 <option value="built_in">Built-In</option>
|
|
|
78 <option value="input_ref">Your Upload File</option>
|
|
|
79 </param>
|
|
|
80 <when value="built_in">
|
|
|
81 <param name="dbkey" type="select" format="text" >
|
|
|
82 <label>Database</label>
|
|
|
83 <options from_file="pepxml_databases.loc">
|
|
|
84 <column name="name" index="0" />
|
|
|
85 <column name="value" index="2" />
|
|
|
86 </options>
|
|
|
87 </param>
|
|
|
88 </when>
|
|
|
89 <when value="input_ref">
|
|
|
90 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
|
|
|
91 </when>
|
|
|
92 </conditional>
|
|
|
93
|
|
|
94 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
|
|
|
95
|
|
|
96
|
|
8
|
97 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
|
|
0
|
98 <options from_file="msgfplus_mods.loc">
|
|
|
99 <column name="name" index="0" />
|
|
|
100 <column name="value" index="2" />
|
|
|
101 </options>
|
|
|
102 </param>
|
|
|
103
|
|
|
104 <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
|
|
|
105 <param name="custom_mod" type="text">
|
|
|
106 </param>
|
|
|
107 </repeat>
|
|
|
108
|
|
|
109
|
|
8
|
110 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
|
|
0
|
111 <options from_file="msgfplus_mods.loc">
|
|
|
112 <column name="name" index="0" />
|
|
|
113 <column name="value" index="2" />
|
|
|
114 </options>
|
|
|
115 </param>
|
|
|
116
|
|
|
117 <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
|
|
|
118 <param name="custom_mod" type="text">
|
|
|
119 </param>
|
|
|
120 </repeat>
|
|
|
121
|
|
|
122
|
|
|
123
|
|
|
124 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
|
|
|
125 <label>Missed Cleavages Allowed</label>
|
|
|
126 <option value="0">0</option>
|
|
|
127 <option value="1">1</option>
|
|
|
128 <option value="2">2</option>
|
|
|
129 </param>
|
|
|
130
|
|
|
131 <param name="enzyme" type="select" format="text">
|
|
|
132 <label>Enzyme</label>
|
|
8
|
133 <option value="0">unspecific cleavage</option>
|
|
|
134 <option value="1">Trypsin</option>
|
|
|
135 <option value="2">Chymotrypsin</option>
|
|
|
136 <option value="3">Lys-C</option>
|
|
|
137 <option value="4">Lys-N</option>
|
|
|
138 <option value="5">glutamyl endopeptidase</option>
|
|
|
139 <option value="6">Arg-C</option>
|
|
|
140 <option value="7">Asp-N</option>
|
|
|
141 <option value="8">alphaLP</option>
|
|
|
142 <option value="9">no cleavage</option>
|
|
0
|
143 </param>
|
|
|
144
|
|
|
145 <param name="instrument" type="select" format="text">
|
|
|
146 <label>Instrument Type</label>
|
|
|
147 <option value="2">TOF</option>
|
|
|
148 <option value="0">Low-res LCQ/LTQ</option>
|
|
|
149 <option value="1">High-res LTQ</option>
|
|
|
150 </param>
|
|
|
151
|
|
8
|
152 <param name="fragment_method" type="select" format="text">
|
|
|
153 <label>Fragmentation Method</label>
|
|
|
154 <option value="0">Respect Input File</option>
|
|
|
155 <option value="1">CID</option>
|
|
|
156 <option value="2">ETD</option>
|
|
|
157 <option value="3">HCD</option>
|
|
|
158 <option value="4">Merge spectra from same precursor</option>
|
|
|
159 </param>
|
|
|
160
|
|
|
161 <param name="protocol" type="select" format="text">
|
|
|
162 <label>Protocol</label>
|
|
|
163 <option value="0">NoProtocol</option>
|
|
|
164 <option value="1">Phosphorylation</option>
|
|
|
165 <option value="2">iTRAQ</option>
|
|
|
166 <option value="3">iTRAQPhospho</option>
|
|
|
167 </param>
|
|
|
168
|
|
0
|
169 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
|
|
|
170
|
|
|
171 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
|
|
|
172 <param name="precursor_tolu" type="select" format="text">
|
|
|
173 <label>Precursor Ion Tolerance Units</label>
|
|
|
174 <option value="ppm">ppm</option>
|
|
|
175 <option value="Da">Da</option>
|
|
|
176 </param>
|
|
|
177
|
|
8
|
178 <param name="isotope_error_range" help="Takes into account of the error introduced by chooosing a non-monoisotopic peak for fragmentation." type="text" size="80" value="0,1" label="Isotope Error Range"/>
|
|
|
179
|
|
|
180 <param name="min_pep_len" help="" type="integer" value="6" label="Minimum Peptide Length"/>
|
|
|
181 <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/>
|
|
|
182 <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/>
|
|
|
183 <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
|
|
|
184 <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
|
|
|
185 <param name="java_mem" help="Increase this value if you get out of memory errors" type="text" size="80" value="3500M" label="Java Memory Limit"/>
|
|
|
186
|
|
|
187
|
|
|
188 <param name="pepxml_output_use" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
|
|
|
189
|
|
0
|
190 </inputs>
|
|
|
191
|
|
|
192
|
|
8
|
193 <!-- <outputs>
|
|
0
|
194 <data format="raw_pepxml" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/>
|
|
|
195 </outputs>
|
|
8
|
196 -->
|
|
|
197 <outputs>
|
|
|
198 <data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}">
|
|
|
199 <change_format>
|
|
|
200 <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}"/>
|
|
|
201 </change_format>
|
|
|
202 </data>
|
|
|
203 </outputs>
|
|
|
204
|
|
|
205
|
|
|
206 <tests>
|
|
|
207 <test>
|
|
|
208 <param name="source_select" value="input_ref"/>
|
|
|
209 <param name="fasta_file" value="bsa.fasta"/>
|
|
|
210 <param name="input_file" value="bsa.mzML"/>
|
|
|
211 <output name="output" file="bsa.mzid" compare="sim_size" delta="600" />
|
|
|
212 </test>
|
|
|
213 </tests>
|
|
0
|
214
|
|
|
215
|
|
|
216 <help>
|
|
|
217
|
|
|
218 **What it does**
|
|
|
219
|
|
|
220 Runs an MS/MS database search using the MSGFPlus search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
|
|
|
221
|
|
|
222 ----
|
|
|
223
|
|
|
224 **References**
|
|
|
225
|
|
|
226 Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm
|
|
|
227
|
|
|
228 </help>
|
|
|
229
|
|
|
230 </tool>
|
