annotate msgfplus_search.xml @ 14:32365fec702c draft

Uploaded
author iracooke
date Thu, 26 Jun 2014 11:39:21 -0400
parents c1df871ffa3c
children 6c751c59ce18
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
10
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.3">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
2 <description>Run an MSGF+ Search</description>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
3 <requirements>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
4 <requirement type="package" version="1.3">protk</requirement>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
5 <requirement type="package" version="20140210">msgfplus</requirement>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
6 <requirement type="package" version="3_0_4388">proteowizard</requirement>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
7 </requirements>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
8 <command>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
9 msgfplus_search.rb
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
10 #if $database.source_select=="built_in":
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
11 --galaxy -d $database.dbkey
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
12 #else
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
13 --galaxy -d $database.fasta_file
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
14 #end if
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
15
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
16 --var-mods='
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
17 $variable_mods
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
18 #for $custom_variable_mod in $custom_variable_mods:
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
19 ,${custom_variable_mod.custom_mod}
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
20 #end for
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
21 '
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
22
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
23 --fix-mods='
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
24 $fixed_mods
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
25 #for $custom_fix_mod in $custom_fix_mods:
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
26 ,${custom_fix_mod.custom_mod}
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
27 #end for
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
28 '
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
29
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
30 $input_file
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
31 -o $output
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
32 -r
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
33 --enzyme=$enzyme
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
34 --precursor-ion-tol-units=$precursor_tolu
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
35 -v $missed_cleavages
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
36 $cleavage_semi
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
37 -p $precursor_ion_tol
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
38 --instrument=$instrument
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
39 --isotope-error-range=$isotope_error_range
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
40 --fragment-method=$fragment_method
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
41 --protocol=$protocol
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
42 --min-pep-len=$min_pep_len
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
43 --max-pep-len=$max_pep_len
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
44 --max-pep-charge=$max_pep_charge
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
45 --min-pep-charge=$min_pep_charge
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
46 --num-reported-matches=$num_reported_matches
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
47 --java-mem=$java_mem
12
49231acb2258 Uploaded
iracooke
parents: 11
diff changeset
48 #if $pepxml_output_use:
49231acb2258 Uploaded
iracooke
parents: 11
diff changeset
49 --pepxml
13
c1df871ffa3c Uploaded
iracooke
parents: 12
diff changeset
50 #end if
10
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
51 </command>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
52
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
53 <inputs>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
54 <conditional name="database">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
55 <param name="source_select" type="select" label="Database source">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
56 <option value="built_in">Built-In</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
57 <option value="input_ref" selected="true">Your Upload File</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
58 </param>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
59 <when value="built_in">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
60 <param name="dbkey" type="select" format="text" >
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
61 <label>Database</label>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
62 <options from_file="pepxml_databases.loc">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
63 <column name="name" index="0" />
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
64 <column name="value" index="2" />
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
65 </options>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
66 </param>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
67 </when>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
68 <when value="input_ref">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
69 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
70 </when>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
71 </conditional>
14
32365fec702c Uploaded
iracooke
parents: 13
diff changeset
72 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
10
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
73 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
74 <options from_file="msgfplus_mods.loc">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
75 <column name="name" index="0" />
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
76 <column name="value" index="2" />
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
77 </options>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
78 </param>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
79 <repeat name="custom_variable_mods" title="Custom Variable Modifications"
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
80 help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
81 <param name="custom_mod" type="text" />
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
82 </repeat>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
83 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
84 <options from_file="msgfplus_mods.loc">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
85 <column name="name" index="0" />
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
86 <column name="value" index="2" />
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
87 </options>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
88 </param>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
89 <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">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
90 <param name="custom_mod" type="text">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
91 </param>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
92 </repeat>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
93 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
94 <label>Missed Cleavages Allowed</label>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
95 <option value="0">0</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
96 <option value="1">1</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
97 <option value="2">2</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
98 </param>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
99
11
deb61a965680 Uploaded
iracooke
parents: 10
diff changeset
100 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue="" />
10
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
101
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
102 <param name="enzyme" type="select" format="text">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
103 <label>Enzyme</label>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
104 <option value="0">unspecific cleavage</option>
12
49231acb2258 Uploaded
iracooke
parents: 11
diff changeset
105 <option value="1" selected="true">Trypsin</option>
10
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
106 <option value="2">Chymotrypsin</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
107 <option value="3">Lys-C</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
108 <option value="4">Lys-N</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
109 <option value="5">glutamyl endopeptidase</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
110 <option value="6">Arg-C</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
111 <option value="7">Asp-N</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
112 <option value="8">alphaLP</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
113 <option value="9">no cleavage</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
114 </param>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
115
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
116 <param name="instrument" type="select" format="text">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
117 <label>Instrument Type</label>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
118 <option value="2">TOF</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
119 <option value="0">Low-res LCQ/LTQ</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
120 <option value="1">High-res LTQ</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
121 </param>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
122
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
123 <param name="fragment_method" type="select" format="text">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
124 <label>Fragmentation Method</label>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
125 <option value="0">Respect Input File</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
126 <option value="1">CID</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
127 <option value="2">ETD</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
128 <option value="3">HCD</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
129 <option value="4">Merge spectra from same precursor</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
130 </param>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
131
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
132 <param name="protocol" type="select" format="text">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
133 <label>Protocol</label>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
134 <option value="0">NoProtocol</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
135 <option value="1">Phosphorylation</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
136 <option value="2">iTRAQ</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
137 <option value="3">iTRAQPhospho</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
138 </param>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
139
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
140 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
141 <param name="precursor_tolu" type="select" format="text">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
142 <label>Precursor Ion Tolerance Units</label>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
143 <option value="ppm">ppm</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
144 <option value="Da">Da</option>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
145 </param>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
146
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
147 <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"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
148 <param name="min_pep_len" help="" type="integer" value="6" label="Minimum Peptide Length"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
149 <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
150 <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
151 <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
152 <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
153 <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"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
154 <param name="pepxml_output_use" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
155 </inputs>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
156 <outputs>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
157 <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}.${input_file.display_name}">
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
158 <change_format>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
159 <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file"
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
160 label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
161 </change_format>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
162 </data>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
163 </outputs>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
164 <tests>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
165 <test>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
166 <param name="source_select" value="input_ref"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
167 <param name="fasta_file" value="bsa.fasta"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
168 <param name="input_file" value="bsa.mzML"/>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
169 <output name="output" file="bsa.mzid" compare="sim_size" delta="600" />
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
170 </test>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
171 </tests>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
172 <help>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
173
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
174 **What it does**
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
175
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
176 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.
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
177
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
178 ----
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
179
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
180 **References**
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
181
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
182 Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
183
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
184 </help>
86daefc0e88d Uploaded
iracooke
parents:
diff changeset
185 </tool>