annotate tandem.xml @ 13:c60d1f18fd85 draft

Uploaded
author iracooke
date Tue, 01 Jul 2014 11:06:33 -0400
parents 618d74240c7f
children 9d6e0ad4d600
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
618d74240c7f Uploaded
iracooke
parents:
diff changeset
1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.2">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
2
618d74240c7f Uploaded
iracooke
parents:
diff changeset
3 <requirements>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
4 <requirement type="package" version="1.3.0">protk</requirement>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
5 </requirements>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
6
618d74240c7f Uploaded
iracooke
parents:
diff changeset
7 <description>Run an X!Tandem Search</description>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
8
618d74240c7f Uploaded
iracooke
parents:
diff changeset
9 <command>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
10 #if $database.source_select=="built_in":
618d74240c7f Uploaded
iracooke
parents:
diff changeset
11 tandem_search.rb -d $database.dbkey
618d74240c7f Uploaded
iracooke
parents:
diff changeset
12 #else
618d74240c7f Uploaded
iracooke
parents:
diff changeset
13 tandem_search.rb -d $database.fasta_file
618d74240c7f Uploaded
iracooke
parents:
diff changeset
14 #end if
618d74240c7f Uploaded
iracooke
parents:
diff changeset
15
618d74240c7f Uploaded
iracooke
parents:
diff changeset
16 #if $tandem_params.source_select=="built_in":
618d74240c7f Uploaded
iracooke
parents:
diff changeset
17 -T $tandem_params.paramskey
618d74240c7f Uploaded
iracooke
parents:
diff changeset
18 #else
618d74240c7f Uploaded
iracooke
parents:
diff changeset
19 -T $tandem_params.params_file
618d74240c7f Uploaded
iracooke
parents:
diff changeset
20 #end if
618d74240c7f Uploaded
iracooke
parents:
diff changeset
21
618d74240c7f Uploaded
iracooke
parents:
diff changeset
22
618d74240c7f Uploaded
iracooke
parents:
diff changeset
23 --var-mods='
618d74240c7f Uploaded
iracooke
parents:
diff changeset
24 $variable_mods
618d74240c7f Uploaded
iracooke
parents:
diff changeset
25 #for $custom_variable_mod in $custom_variable_mods:
618d74240c7f Uploaded
iracooke
parents:
diff changeset
26 ,${custom_variable_mod.custom_mod}
618d74240c7f Uploaded
iracooke
parents:
diff changeset
27 #end for
618d74240c7f Uploaded
iracooke
parents:
diff changeset
28 '
618d74240c7f Uploaded
iracooke
parents:
diff changeset
29
618d74240c7f Uploaded
iracooke
parents:
diff changeset
30 --fix-mods='
618d74240c7f Uploaded
iracooke
parents:
diff changeset
31 $fixed_mods
618d74240c7f Uploaded
iracooke
parents:
diff changeset
32 #for $custom_fix_mod in $custom_fix_mods:
618d74240c7f Uploaded
iracooke
parents:
diff changeset
33 ,${custom_fix_mod.custom_mod}
618d74240c7f Uploaded
iracooke
parents:
diff changeset
34 #end for
618d74240c7f Uploaded
iracooke
parents:
diff changeset
35 '
618d74240c7f Uploaded
iracooke
parents:
diff changeset
36
618d74240c7f Uploaded
iracooke
parents:
diff changeset
37 $input_file -o $output -r
618d74240c7f Uploaded
iracooke
parents:
diff changeset
38
618d74240c7f Uploaded
iracooke
parents:
diff changeset
39 --enzyme=$enzyme
618d74240c7f Uploaded
iracooke
parents:
diff changeset
40
618d74240c7f Uploaded
iracooke
parents:
diff changeset
41 --precursor-ion-tol-units=$precursor_tolu
618d74240c7f Uploaded
iracooke
parents:
diff changeset
42
618d74240c7f Uploaded
iracooke
parents:
diff changeset
43 -v $missed_cleavages
618d74240c7f Uploaded
iracooke
parents:
diff changeset
44
618d74240c7f Uploaded
iracooke
parents:
diff changeset
45 -f $fragment_ion_tol
618d74240c7f Uploaded
iracooke
parents:
diff changeset
46
618d74240c7f Uploaded
iracooke
parents:
diff changeset
47 -p $precursor_ion_tol
618d74240c7f Uploaded
iracooke
parents:
diff changeset
48
618d74240c7f Uploaded
iracooke
parents:
diff changeset
49 $allow_multi_isotope_search
618d74240c7f Uploaded
iracooke
parents:
diff changeset
50
618d74240c7f Uploaded
iracooke
parents:
diff changeset
51 $acetyl_protein_nterm
618d74240c7f Uploaded
iracooke
parents:
diff changeset
52
618d74240c7f Uploaded
iracooke
parents:
diff changeset
53 $cleavage_semi
618d74240c7f Uploaded
iracooke
parents:
diff changeset
54
618d74240c7f Uploaded
iracooke
parents:
diff changeset
55 $keep_spectra
618d74240c7f Uploaded
iracooke
parents:
diff changeset
56
618d74240c7f Uploaded
iracooke
parents:
diff changeset
57 --threads $threads
618d74240c7f Uploaded
iracooke
parents:
diff changeset
58
618d74240c7f Uploaded
iracooke
parents:
diff changeset
59 </command>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
60
618d74240c7f Uploaded
iracooke
parents:
diff changeset
61 <inputs>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
62 <conditional name="database">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
63 <param name="source_select" type="select" label="Database source">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
64 <option value="built_in">Built-In</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
65 <option value="input_ref" selected="true">Your Upload File</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
66 </param>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
67 <when value="built_in">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
68 <param name="dbkey" type="select" format="text" >
618d74240c7f Uploaded
iracooke
parents:
diff changeset
69 <label>Database</label>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
70 <options from_file="pepxml_databases.loc">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
71 <column name="name" index="0" />
618d74240c7f Uploaded
iracooke
parents:
diff changeset
72 <column name="value" index="2" />
618d74240c7f Uploaded
iracooke
parents:
diff changeset
73 </options>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
74 </param>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
75 </when>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
76 <when value="input_ref">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
77 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
618d74240c7f Uploaded
iracooke
parents:
diff changeset
78 </when>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
79 </conditional>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
80
618d74240c7f Uploaded
iracooke
parents:
diff changeset
81 <conditional name="tandem_params">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
82 <param name="source_select" type="select" label="Baseline Parameters">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
83 <option value="built_in" selected="true">Built-In</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
84 <option value="input_ref">Custom parameter file</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
85 </param>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
86 <when value="built_in">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
87 <param name="paramskey" type="select" format="text" >
618d74240c7f Uploaded
iracooke
parents:
diff changeset
88 <label>Paramset</label>
13
c60d1f18fd85 Uploaded
iracooke
parents: 11
diff changeset
89 <option value="gpm">GPM</option>
11
618d74240c7f Uploaded
iracooke
parents:
diff changeset
90 <option value="isb_native">ISB Native</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
91 <option value="isb_kscore">ISB K-Score</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
92 </param>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
93 </when>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
94 <when value="input_ref">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
95 <param name="params_file" type="data" format="xml" label="Custom X!Tandem Parameters" />
618d74240c7f Uploaded
iracooke
parents:
diff changeset
96 </when>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
97 </conditional>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
98
618d74240c7f Uploaded
iracooke
parents:
diff changeset
99 <param name="input_file" type="data" format="mzml,mgf" multiple="false" label="MSMS File" help="A file with MS/MS data"/>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
100
618d74240c7f Uploaded
iracooke
parents:
diff changeset
101 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
618d74240c7f Uploaded
iracooke
parents:
diff changeset
102 clicking to select multiple items">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
103 <options from_file="tandem_mods.loc">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
104 <column name="name" index="0" />
618d74240c7f Uploaded
iracooke
parents:
diff changeset
105 <column name="value" index="2" />
618d74240c7f Uploaded
iracooke
parents:
diff changeset
106 </options>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
107 </param>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
108
618d74240c7f Uploaded
iracooke
parents:
diff changeset
109 <repeat name="custom_variable_mods" title="Custom Variable Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
110 <param name="custom_mod" type="text">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
111 </param>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
112 </repeat>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
113
618d74240c7f Uploaded
iracooke
parents:
diff changeset
114
618d74240c7f Uploaded
iracooke
parents:
diff changeset
115 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
618d74240c7f Uploaded
iracooke
parents:
diff changeset
116 clicking to select multiple items">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
117 <options from_file="tandem_mods.loc">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
118 <column name="name" index="0" />
618d74240c7f Uploaded
iracooke
parents:
diff changeset
119 <column name="value" index="2" />
618d74240c7f Uploaded
iracooke
parents:
diff changeset
120 </options>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
121 </param>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
122
618d74240c7f Uploaded
iracooke
parents:
diff changeset
123 <repeat name="custom_fix_mods" title="Custom Fixed Modifications" help="You can specify a modification when present in a motif. For instance, 0.998@N!{P}[ST] is a deamidation modification on N only if it is present in an N[any but P][S or T] motif (N-glycosite).">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
124 <param name="custom_mod" type="text">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
125 </param>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
126 </repeat>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
127
618d74240c7f Uploaded
iracooke
parents:
diff changeset
128 <param name="acetyl_protein_nterm" type="boolean" label="Allow N-terminal protein acetylation as a variable modification" truevalue="-y" falsevalue="" />
618d74240c7f Uploaded
iracooke
parents:
diff changeset
129
618d74240c7f Uploaded
iracooke
parents:
diff changeset
130
618d74240c7f Uploaded
iracooke
parents:
diff changeset
131 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
132 <label>Missed Cleavages Allowed</label>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
133 <option value="0">0</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
134 <option value="1">1</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
135 <option value="2">2</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
136 </param>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
137
618d74240c7f Uploaded
iracooke
parents:
diff changeset
138 <param name="cleavage_semi" type="boolean" label="Allow semi-cleaved peptides" help="This can increase search time dramatically" truevalue="--cleavage-semi" falsevalue=""/>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
139
618d74240c7f Uploaded
iracooke
parents:
diff changeset
140 <param name="keep_spectra" type="boolean" label="Keep Spectra" help="Include spectra in the output" truevalue="--output-spectra" falsevalue=""/>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
141
618d74240c7f Uploaded
iracooke
parents:
diff changeset
142 <param name="threads" type="integer" value="1" label="Threads" help="Number of threads to use for search. Maximum is 16"/>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
143
618d74240c7f Uploaded
iracooke
parents:
diff changeset
144 <param name="enzyme" type="select" format="text">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
145 <label>Enzyme</label>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
146 <option value="[R]|{P}">argc - [R]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
147 <option value="[X]|[D]">aspn - [X]|[D]</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
148 <option value="[FLMWY]|{P}">chymotrypsin - [FLMWY]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
149 <option value="[R]|[X]">clostripain - [R]|[X]</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
150 <option value="[M]|{P}">cnbr - [M]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
151 <option value="[AGILV]|{P}">elastase - [AGILV]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
152 <option value="[D]|{P}">formicacid - [D]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
153 <option value="[DE]|{P}">gluc - [DE]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
154 <option value="[E]|{P}">gluc_bicarb - [E]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
155 <option value="[W]|[X]">iodosobenzoate - [W]|[X]</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
156 <option value="[K]|{P}">lysc - [K]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
157 <option value="[K]|[X]">lysc-p - [K]|[X]</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
158 <option value="[X]|[K]">lysn - [X]|[K]</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
159 <option value="[X]|[AKRS]">lysn_promisc - [X]|[AKRS]</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
160 <option value="[X]|[X]">nonspecific - [X]|[X]</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
161 <option value="[FL]|[X]">pepsina - [FL]|[X]</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
162 <option value="[P]|[X]">protein_endopeptidase - [P]|[X]</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
163 <option value="[E]|[X]">staph_protease - [E]|[X]</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
164 <option value="[FMWY]|{P},[KR]|{P},[X]|[D]">tca - [FMWY]|{P},[KR]|{P},[X]|[D]</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
165 <option value="[KR]|{P}" selected="true">trypsin - [KR]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
166 <option value="[FKLMRWY]|{P}">trypsin/chymotrypsin - [FKLMRWY]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
167 <option value="[KR]|{P},[M]|{P}">trypsin/cnbr - [KR]|{P},[M]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
168 <option value="[DEKR]|{P}">trypsin_gluc - [DEKR]|{P}</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
169 </param>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
170
618d74240c7f Uploaded
iracooke
parents:
diff changeset
171
618d74240c7f Uploaded
iracooke
parents:
diff changeset
172 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
173
618d74240c7f Uploaded
iracooke
parents:
diff changeset
174 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
175 <param name="precursor_tolu" type="select" format="text">
618d74240c7f Uploaded
iracooke
parents:
diff changeset
176 <label>Precursor Ion Tolerance Units</label>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
177 <option value="ppm">ppm</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
178 <option value="Da">Da</option>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
179 </param>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
180
618d74240c7f Uploaded
iracooke
parents:
diff changeset
181 <param name="allow_multi_isotope_search" type="boolean" label="Allow multi-isotope search" help="This allows peptide candidates in windows around -1 Da and -2 Da from the acquired mass to be considered. Only applicable when the minus/plus window above is set to less than 0.5 Da. Good for accurate-mass instruments for which the reported precursor mass is not corrected to the monoisotopic mass." truevalue="" falsevalue=""/>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
182
618d74240c7f Uploaded
iracooke
parents:
diff changeset
183 </inputs>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
184
618d74240c7f Uploaded
iracooke
parents:
diff changeset
185
618d74240c7f Uploaded
iracooke
parents:
diff changeset
186 <outputs>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
187 <data format="tandem" name="output" metadata_source="input_file" label="X!Tandem_vs_${database.dbkey if $database.has_key('dbkey') else $database.fasta_file.display_name}.${input_file.display_name}.${input_file.display_name}.tandem"/>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
188 </outputs>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
189
618d74240c7f Uploaded
iracooke
parents:
diff changeset
190
618d74240c7f Uploaded
iracooke
parents:
diff changeset
191 <help>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
192
618d74240c7f Uploaded
iracooke
parents:
diff changeset
193 **What it does**
618d74240c7f Uploaded
iracooke
parents:
diff changeset
194
618d74240c7f Uploaded
iracooke
parents:
diff changeset
195 Runs an MS/MS database search using the X!Tandem search engine. Output is in the form of a pepXML file containing identified peptides along with their raw search scores.
618d74240c7f Uploaded
iracooke
parents:
diff changeset
196
618d74240c7f Uploaded
iracooke
parents:
diff changeset
197 ----
618d74240c7f Uploaded
iracooke
parents:
diff changeset
198
618d74240c7f Uploaded
iracooke
parents:
diff changeset
199 **References**
618d74240c7f Uploaded
iracooke
parents:
diff changeset
200
618d74240c7f Uploaded
iracooke
parents:
diff changeset
201 Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
618d74240c7f Uploaded
iracooke
parents:
diff changeset
202
618d74240c7f Uploaded
iracooke
parents:
diff changeset
203 </help>
618d74240c7f Uploaded
iracooke
parents:
diff changeset
204
618d74240c7f Uploaded
iracooke
parents:
diff changeset
205 </tool>