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comparison msgfplus_search.xml @ 10:86daefc0e88d draft

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author iracooke
date Fri, 13 Jun 2014 18:36:52 -0400
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9:e0a1e8a0500a 10:86daefc0e88d
1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.3">
2 <description>Run an MSGF+ Search</description>
3 <requirements>
4 <requirement type="package" version="1.3">protk</requirement>
5 <requirement type="package" version="20140210">msgfplus</requirement>
6 <requirement type="package" version="3_0_4388">proteowizard</requirement>
7 </requirements>
8 <command>
9 msgfplus_search.rb
10 #if $database.source_select=="built_in":
11 --galaxy -d $database.dbkey
12 #else
13 --galaxy -d $database.fasta_file
14 #end if
15
16 --var-mods='
17 $variable_mods
18 #for $custom_variable_mod in $custom_variable_mods:
19 ,${custom_variable_mod.custom_mod}
20 #end for
21 '
22
23 --fix-mods='
24 $fixed_mods
25 #for $custom_fix_mod in $custom_fix_mods:
26 ,${custom_fix_mod.custom_mod}
27 #end for
28 '
29
30 $input_file
31 -o $output
32 -r
33 --enzyme=$enzyme
34 --precursor-ion-tol-units=$precursor_tolu
35 -v $missed_cleavages
36 $cleavage_semi
37 -f $fragment_ion_tol
38 -p $precursor_ion_tol
39 --instrument=$instrument
40 --isotope-error-range=$isotope_error_range
41 --fragment-method=$fragment_method
42 --protocol=$protocol
43 --min-pep-len=$min_pep_len
44 --max-pep-len=$max_pep_len
45 --max-pep-charge=$max_pep_charge
46 --min-pep-charge=$min_pep_charge
47 --num-reported-matches=$num_reported_matches
48 --java-mem=$java_mem
49 #unless $pepxml_output_use:
50 --no-pepxml
51 #end unless
52 </command>
53
54 <inputs>
55 <conditional name="database">
56 <param name="source_select" type="select" label="Database source">
57 <option value="built_in">Built-In</option>
58 <option value="input_ref" selected="true">Your Upload File</option>
59 </param>
60 <when value="built_in">
61 <param name="dbkey" type="select" format="text" >
62 <label>Database</label>
63 <options from_file="pepxml_databases.loc">
64 <column name="name" index="0" />
65 <column name="value" index="2" />
66 </options>
67 </param>
68 </when>
69 <when value="input_ref">
70 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
71 </when>
72 </conditional>
73 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
74 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
75 <options from_file="msgfplus_mods.loc">
76 <column name="name" index="0" />
77 <column name="value" index="2" />
78 </options>
79 </param>
80 <repeat name="custom_variable_mods" title="Custom Variable Modifications"
81 help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
82 <param name="custom_mod" type="text" />
83 </repeat>
84 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
85 <options from_file="msgfplus_mods.loc">
86 <column name="name" index="0" />
87 <column name="value" index="2" />
88 </options>
89 </param>
90 <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">
91 <param name="custom_mod" type="text">
92 </param>
93 </repeat>
94 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
95 <label>Missed Cleavages Allowed</label>
96 <option value="0">0</option>
97 <option value="1">1</option>
98 <option value="2">2</option>
99 </param>
100
101 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="" falsevalue="--no-cleavage-semi" />
102
103 <param name="enzyme" type="select" format="text">
104 <label>Enzyme</label>
105 <option value="0">unspecific cleavage</option>
106 <option value="1">Trypsin</option>
107 <option value="2">Chymotrypsin</option>
108 <option value="3">Lys-C</option>
109 <option value="4">Lys-N</option>
110 <option value="5">glutamyl endopeptidase</option>
111 <option value="6">Arg-C</option>
112 <option value="7">Asp-N</option>
113 <option value="8">alphaLP</option>
114 <option value="9">no cleavage</option>
115 </param>
116
117 <param name="instrument" type="select" format="text">
118 <label>Instrument Type</label>
119 <option value="2">TOF</option>
120 <option value="0">Low-res LCQ/LTQ</option>
121 <option value="1">High-res LTQ</option>
122 </param>
123
124 <param name="fragment_method" type="select" format="text">
125 <label>Fragmentation Method</label>
126 <option value="0">Respect Input File</option>
127 <option value="1">CID</option>
128 <option value="2">ETD</option>
129 <option value="3">HCD</option>
130 <option value="4">Merge spectra from same precursor</option>
131 </param>
132
133 <param name="protocol" type="select" format="text">
134 <label>Protocol</label>
135 <option value="0">NoProtocol</option>
136 <option value="1">Phosphorylation</option>
137 <option value="2">iTRAQ</option>
138 <option value="3">iTRAQPhospho</option>
139 </param>
140
141 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
142
143 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
144 <param name="precursor_tolu" type="select" format="text">
145 <label>Precursor Ion Tolerance Units</label>
146 <option value="ppm">ppm</option>
147 <option value="Da">Da</option>
148 </param>
149
150 <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"/>
151 <param name="min_pep_len" help="" type="integer" value="6" label="Minimum Peptide Length"/>
152 <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/>
153 <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/>
154 <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
155 <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
156 <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"/>
157 <param name="pepxml_output_use" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
158 </inputs>
159 <outputs>
160 <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}.${input_file.display_name}">
161 <change_format>
162 <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file"
163 label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}"/>
164 </change_format>
165 </data>
166 </outputs>
167 <tests>
168 <test>
169 <param name="source_select" value="input_ref"/>
170 <param name="fasta_file" value="bsa.fasta"/>
171 <param name="input_file" value="bsa.mzML"/>
172 <output name="output" file="bsa.mzid" compare="sim_size" delta="600" />
173 </test>
174 </tests>
175 <help>
176
177 **What it does**
178
179 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.
180
181 ----
182
183 **References**
184
185 Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm
186
187 </help>
188 </tool>