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comparison msgfplus_search.xml @ 8:4f6cbe948065

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author Ira Cooke <iracooke@gmail.com>
date Sun, 09 Jun 2013 08:17:57 -0500
parents b3f2bd49029c
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7:b3f2bd49029c 8:4f6cbe948065
1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.1"> 1 <tool id="proteomics_search_msgfplus_1" name="MSGF+ MSMS Search" version="1.0.1">
2 2
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.2.0">galaxy_protk</requirement> 4 <requirement type="package" version="1.2.2">galaxy_protk</requirement>
5 <requirement type="package" version="20130227">msgfplus</requirement> 5 <requirement type="package" version="20130227">msgfplus</requirement>
6 <requirement type="package" version="3_0_4388">proteowizard</requirement> 6 <requirement type="package" version="3_0_4388">proteowizard</requirement>
7 </requirements> 7 </requirements>
8 8
9 9
10 <description>Run an MSGF+ Search</description> 10 <description>Run an MSGF+ Search</description>
11 11
12 <command> 12 <command>
13 rvm 1.9.3@protk-1.2.2 do msgfplus_search.rb
13 #if $database.source_select=="built_in": 14 #if $database.source_select=="built_in":
14 rvm 1.9.3@protk-1.2.0 do msgfplus_search.rb --galaxy -d $database.dbkey 15 --galaxy -d $database.dbkey
15 #else #rvm 1.9.3@protk-1.2.0 do msgfplus_search.rb --galaxy -d $database.fasta_file 16 #else
17 --galaxy -d $database.fasta_file
16 #end if 18 #end if
17 19
18 --var-mods=' 20 --var-mods='
19 $variable_mods 21 $variable_mods
20 #for $custom_variable_mod in $custom_variable_mods: 22 #for $custom_variable_mod in $custom_variable_mods:
27 #for $custom_fix_mod in $custom_fix_mods: 29 #for $custom_fix_mod in $custom_fix_mods:
28 ,${custom_fix_mod.custom_mod} 30 ,${custom_fix_mod.custom_mod}
29 #end for 31 #end for
30 ' 32 '
31 33
32 $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol --instrument=$instrument 34 $input_file
33 35
34 36 -o $output
35 37
38 -r
39
40 --enzyme=$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
51
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
36 </command> 72 </command>
37 73
38 <inputs> 74 <inputs>
39 <conditional name="database"> 75 <conditional name="database">
40 <param name="source_select" type="select" label="Database source"> 76 <param name="source_select" type="select" label="Database source">
56 </conditional> 92 </conditional>
57 93
58 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/> 94 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
59 95
60 96
61 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while 97 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple Selection Allowed">
62 clicking to select multiple items">
63 <options from_file="msgfplus_mods.loc"> 98 <options from_file="msgfplus_mods.loc">
64 <column name="name" index="0" /> 99 <column name="name" index="0" />
65 <column name="value" index="2" /> 100 <column name="value" index="2" />
66 </options> 101 </options>
67 </param> 102 </param>
70 <param name="custom_mod" type="text"> 105 <param name="custom_mod" type="text">
71 </param> 106 </param>
72 </repeat> 107 </repeat>
73 108
74 109
75 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while 110 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple Selection Allowed">
76 clicking to select multiple items">
77 <options from_file="msgfplus_mods.loc"> 111 <options from_file="msgfplus_mods.loc">
78 <column name="name" index="0" /> 112 <column name="name" index="0" />
79 <column name="value" index="2" /> 113 <column name="value" index="2" />
80 </options> 114 </options>
81 </param> 115 </param>
94 <option value="2">2</option> 128 <option value="2">2</option>
95 </param> 129 </param>
96 130
97 <param name="enzyme" type="select" format="text"> 131 <param name="enzyme" type="select" format="text">
98 <label>Enzyme</label> 132 <label>Enzyme</label>
99 <option value="Trypsin">Trypsin</option> 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>
100 </param> 143 </param>
101 144
102 <param name="instrument" type="select" format="text"> 145 <param name="instrument" type="select" format="text">
103 <label>Instrument Type</label> 146 <label>Instrument Type</label>
104 <option value="2">TOF</option> 147 <option value="2">TOF</option>
105 <option value="0">Low-res LCQ/LTQ</option> 148 <option value="0">Low-res LCQ/LTQ</option>
106 <option value="1">High-res LTQ</option> 149 <option value="1">High-res LTQ</option>
107 </param> 150 </param>
108 151
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
109 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/> 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"/>
110 170
111 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/> 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"/>
112 <param name="precursor_tolu" type="select" format="text"> 172 <param name="precursor_tolu" type="select" format="text">
113 <label>Precursor Ion Tolerance Units</label> 173 <label>Precursor Ion Tolerance Units</label>
114 <option value="ppm">ppm</option> 174 <option value="ppm">ppm</option>
115 <option value="Da">Da</option> 175 <option value="Da">Da</option>
116 </param> 176 </param>
117 177
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
118 </inputs> 190 </inputs>
119 191
120 192
121 <outputs> 193 <!-- <outputs>
122 <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}.${input_file.display_name}.pepXML"/> 194 <data format="raw_pepxml" name="output" metadata_source="input_file" label="MSGF+_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.pepXML"/>
123 </outputs> 195 </outputs>
196 -->
197 <outputs>
198 <data format="mzid" name="output" metadata_source="input_file" label="MSGF+_vs_${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>
124 214
125 215
126 <help> 216 <help>
127 217
128 **What it does** 218 **What it does**