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comparison msgfplus_search.xml @ 8:dfb2b78b3aff draft

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author simonalpha
date Mon, 05 Jan 2015 17:17:45 -0500
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7:9ee2e20c6f1a 8:dfb2b78b3aff
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 <container type="docker">simonalpha/protk:1.4.0</container>
5 <requirement type="package" version="1.3">protk</requirement>
6 <requirement type="package" version="20140210">msgfplus</requirement>
7 <requirement type="package" version="3_0_4388">proteowizard</requirement>
8 </requirements>
9 <command>
10 msgfplus_search.rb
11 #if $database.source_select=="built_in":
12 --galaxy -d $database.dbkey
13 #else
14 --galaxy -d $database.fasta_file
15 #end if
16
17 --var-mods='
18 $variable_mods
19 #for $custom_variable_mod in $custom_variable_mods:
20 ,${custom_variable_mod.custom_mod}
21 #end for
22 '
23
24 --fix-mods='
25 $fixed_mods
26 #for $custom_fix_mod in $custom_fix_mods:
27 ,${custom_fix_mod.custom_mod}
28 #end for
29 '
30
31 $input_file
32 -o $output
33 -r
34 --enzyme=$enzyme
35 --precursor-ion-tol-units=$precursor_tolu
36 -v $missed_cleavages
37 $cleavage_semi
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
50 --threads $threads
51
52 #if $pepxml_output_use:
53 --pepxml
54 #end if
55 </command>
56
57 <inputs>
58 <conditional name="database">
59 <param name="source_select" type="select" label="Database source">
60 <option value="built_in">Built-In</option>
61 <option value="input_ref" selected="true">Your Upload File</option>
62 </param>
63 <when value="built_in">
64 <param name="dbkey" type="select" format="text" >
65 <label>Database</label>
66 <options from_file="pepxml_databases.loc">
67 <column name="name" index="0" />
68 <column name="value" index="2" />
69 </options>
70 </param>
71 </when>
72 <when value="input_ref">
73 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
74 </when>
75 </conditional>
76 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
77 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
78 <options from_file="msgfplus_mods.loc">
79 <column name="name" index="0" />
80 <column name="value" index="2" />
81 </options>
82 </param>
83 <repeat name="custom_variable_mods" title="Custom Variable Modifications"
84 help="See https://bix-lab.ucsd.edu/pages/viewpage.action?pageId=13533355 for details on how to create these">
85 <param name="custom_mod" type="text" />
86 </repeat>
87 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
88 <options from_file="msgfplus_mods.loc">
89 <column name="name" index="0" />
90 <column name="value" index="2" />
91 </options>
92 </param>
93 <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">
94 <param name="custom_mod" type="text">
95 </param>
96 </repeat>
97 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
98 <label>Missed Cleavages Allowed</label>
99 <option value="0">0</option>
100 <option value="1">1</option>
101 <option selected="true" value="2">2</option>
102 </param>
103
104 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue="" />
105
106 <param name="enzyme" type="select" format="text">
107 <label>Enzyme</label>
108 <option value="0">unspecific cleavage</option>
109 <option value="1" selected="true">Trypsin</option>
110 <option value="2">Chymotrypsin</option>
111 <option value="3">Lys-C</option>
112 <option value="4">Lys-N</option>
113 <option value="5">glutamyl endopeptidase</option>
114 <option value="6">Arg-C</option>
115 <option value="7">Asp-N</option>
116 <option value="8">alphaLP</option>
117 <option value="9">no cleavage</option>
118 </param>
119
120 <param name="instrument" type="select" format="text">
121 <label>Instrument Type</label>
122 <option value="2">TOF</option>
123 <option value="0" selected="true">Low-res LCQ/LTQ</option>
124 <option value="1">High-res LTQ</option>
125 </param>
126
127 <param name="fragment_method" type="select" format="text">
128 <label>Fragmentation Method</label>
129 <option value="0">Respect Input File</option>
130 <option value="1">CID</option>
131 <option value="2">ETD</option>
132 <option value="3">HCD</option>
133 <option value="4">Merge spectra from same precursor</option>
134 </param>
135
136 <param name="protocol" type="select" format="text">
137 <label>Protocol</label>
138 <option value="0">NoProtocol</option>
139 <option value="1">Phosphorylation</option>
140 <option value="2">iTRAQ</option>
141 <option value="3">iTRAQPhospho</option>
142 </param>
143
144 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" label="Precursor ion tolerance"/>
145 <param name="precursor_tolu" type="select" format="text">
146 <label>Precursor Ion Tolerance Units</label>
147 <option value="ppm">ppm</option>
148 <option value="Da">Da</option>
149 </param>
150
151 <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"/>
152 <param name="min_pep_len" help="" type="integer" value="6" label="Minimum Peptide Length"/>
153 <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/>
154 <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/>
155 <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
156 <param name="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
157 <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"/>
158 <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search."/>
159 <param name="pepxml_output_use" checked="true" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" />
160 </inputs>
161 <outputs>
162 <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}.${input_file.display_name}.${'pepXML' if $pepxml_output_use else 'mzid'}">
163 <change_format>
164 <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file"/>
165 </change_format>
166 </data>
167 </outputs>
168 <tests>
169 <test>
170 <param name="source_select" value="input_ref"/>
171 <param name="fasta_file" value="bsa.fasta"/>
172 <param name="input_file" value="bsa.mzML"/>
173 <output name="output" file="bsa.mzid" compare="sim_size" delta="600" />
174 </test>
175 </tests>
176 <help>
177
178 **What it does**
179
180 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.
181
182 ----
183
184 **References**
185
186 Please see http://proteomics.ucsd.edu/Software/MSGFPlus.html for details of the MSGFPlus search engine and references describing its algorithm
187
188 </help>
189 </tool>