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