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comparison msgfplus_search.xml @ 15:6c751c59ce18 draft

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Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 20:04:30 -0400
parents 32365fec702c
children 66a149ef79f7
comparison
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14:32365fec702c 15:6c751c59ce18
1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.3"> 1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.1.0">
2 <description>Run an MSGF+ Search</description> 2 <description>Run an MSGF+ Search</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3">protk</requirement> 4 <container type="docker">iracooke/protk-1.4.1</container>
5 <requirement type="package" version="1.4">protk</requirement>
5 <requirement type="package" version="20140210">msgfplus</requirement> 6 <requirement type="package" version="20140210">msgfplus</requirement>
6 <requirement type="package" version="3_0_4388">proteowizard</requirement> 7 <requirement type="package" version="3_0_4388">proteowizard</requirement>
7 </requirements> 8 </requirements>
8 <command> 9 <command>
9 msgfplus_search.rb 10 msgfplus_search.rb
43 --max-pep-len=$max_pep_len 44 --max-pep-len=$max_pep_len
44 --max-pep-charge=$max_pep_charge 45 --max-pep-charge=$max_pep_charge
45 --min-pep-charge=$min_pep_charge 46 --min-pep-charge=$min_pep_charge
46 --num-reported-matches=$num_reported_matches 47 --num-reported-matches=$num_reported_matches
47 --java-mem=$java_mem 48 --java-mem=$java_mem
49
50 --threads $threads
51
48 #if $pepxml_output_use: 52 #if $pepxml_output_use:
49 --pepxml 53 --pepxml
50 #end if 54 #end if
51 </command> 55 </command>
52 56
92 </repeat> 96 </repeat>
93 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites"> 97 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
94 <label>Missed Cleavages Allowed</label> 98 <label>Missed Cleavages Allowed</label>
95 <option value="0">0</option> 99 <option value="0">0</option>
96 <option value="1">1</option> 100 <option value="1">1</option>
97 <option value="2">2</option> 101 <option selected="true" value="2">2</option>
98 </param> 102 </param>
99 103
100 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue="" /> 104 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue="" />
101 105
102 <param name="enzyme" type="select" format="text"> 106 <param name="enzyme" type="select" format="text">
114 </param> 118 </param>
115 119
116 <param name="instrument" type="select" format="text"> 120 <param name="instrument" type="select" format="text">
117 <label>Instrument Type</label> 121 <label>Instrument Type</label>
118 <option value="2">TOF</option> 122 <option value="2">TOF</option>
119 <option value="0">Low-res LCQ/LTQ</option> 123 <option value="0" selected="true">Low-res LCQ/LTQ</option>
120 <option value="1">High-res LTQ</option> 124 <option value="1">High-res LTQ</option>
121 </param> 125 </param>
122 126
123 <param name="fragment_method" type="select" format="text"> 127 <param name="fragment_method" type="select" format="text">
124 <label>Fragmentation Method</label> 128 <label>Fragmentation Method</label>
135 <option value="1">Phosphorylation</option> 139 <option value="1">Phosphorylation</option>
136 <option value="2">iTRAQ</option> 140 <option value="2">iTRAQ</option>
137 <option value="3">iTRAQPhospho</option> 141 <option value="3">iTRAQPhospho</option>
138 </param> 142 </param>
139 143
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"/> 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"/>
141 <param name="precursor_tolu" type="select" format="text"> 145 <param name="precursor_tolu" type="select" format="text">
142 <label>Precursor Ion Tolerance Units</label> 146 <label>Precursor Ion Tolerance Units</label>
143 <option value="ppm">ppm</option> 147 <option value="ppm">ppm</option>
144 <option value="Da">Da</option> 148 <option value="Da">Da</option>
145 </param> 149 </param>
149 <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/> 153 <param name="max_pep_len" help="" type="integer" value="40" label="Maximum Peptide Length"/>
150 <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/> 154 <param name="min_pep_charge" help="" type="integer" value="2" label="Minimum Peptide Charge"/>
151 <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/> 155 <param name="max_pep_charge" help="" type="integer" value="3" label="Maximum Peptide Charge"/>
152 <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="num_reported_matches" help="Number of matches per spectrum to be reported" type="integer" value="1" label="Num reported matches"/>
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"/> 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"/>
154 <param name="pepxml_output_use" type="boolean" label="Convert results to pepXML" help="" truevalue="true" falsevalue="false" /> 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" />
155 </inputs> 160 </inputs>
156 <outputs> 161 <outputs>
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}.${input_file.display_name}"> 162 <data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.${'pepXML' if $pepxml_output_use else 'mzid'}">
158 <change_format> 163 <change_format>
159 <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file" 164 <when input="pepxml_output_use" value="true" format="raw_pepxml" metadata_source="input_file"/>
160 label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}"/>
161 </change_format> 165 </change_format>
162 </data> 166 </data>
163 </outputs> 167 </outputs>
168
164 <tests> 169 <tests>
170 <!-- Just test that the tool runs and produces vaguely correct output -->
165 <test> 171 <test>
166 <param name="source_select" value="input_ref"/> 172 <param name="source_select" value="input_ref"/>
167 <param name="fasta_file" value="bsa.fasta"/> 173 <param name="fasta_file" value="testdb.fasta" format="fasta"/>
168 <param name="input_file" value="bsa.mzML"/> 174 <param name="input_file" value="tiny.mzML" format="mzml"/>
169 <output name="output" file="bsa.mzid" compare="sim_size" delta="600" /> 175 <param name="precursor_ion_tol" value="200"/>
176 <param name="pepxml_output_use" value="true"/>
177 <output name="output" format="raw_pepxml">
178 <assert_contents>
179 <has_text text="FALPQYLKTVYQHQKAMKPWIQPKTKVIPYVRYL" />
180 </assert_contents>
181 </output>
170 </test> 182 </test>
171 </tests> 183 </tests>
184
172 <help> 185 <help>
173 186
174 **What it does** 187 **What it does**
175 188
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. 189 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.