|
0
|
1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.0">
|
|
|
2 <requirements><requirement type="package">protkgem</requirement></requirements>
|
|
|
3 <description>Run an X!Tandem Search</description>
|
|
|
4
|
|
|
5 <command>
|
|
|
6 #if $database.source_select=="built_in":
|
|
|
7 tandem_search.rb -d $database.dbkey
|
|
|
8 #else #tandem_search.rb -d $database.fasta_file
|
|
|
9 #end if
|
|
|
10
|
|
|
11 --var-mods='
|
|
|
12 $variable_mods
|
|
|
13 #for $custom_variable_mod in $custom_variable_mods:
|
|
|
14 ,${custom_variable_mod.custom_mod}
|
|
|
15 #end for
|
|
|
16 '
|
|
|
17
|
|
|
18 --fix-mods='
|
|
|
19 $fixed_mods
|
|
|
20 #for $custom_fix_mod in $custom_fix_mods:
|
|
|
21 ,${custom_fix_mod.custom_mod}
|
|
|
22 #end for
|
|
|
23 '
|
|
|
24
|
|
|
25 $input_file -o $output -r --enzyme=$enzyme --precursor-ion-tol-units=$precursor_tolu -v $missed_cleavages -f $fragment_ion_tol -p $precursor_ion_tol $allow_multi_isotope_search --keep-params-files
|
|
|
26
|
|
|
27
|
|
|
28
|
|
|
29 </command>
|
|
|
30
|
|
|
31 <inputs>
|
|
|
32 <conditional name="database">
|
|
|
33 <param name="source_select" type="select" label="Database source">
|
|
|
34 <option value="built_in">Built-In</option>
|
|
|
35 <option value="input_ref">Your Upload File</option>
|
|
|
36 </param>
|
|
|
37 <when value="built_in">
|
|
|
38 <param name="dbkey" type="select" format="text" >
|
|
|
39 <label>Database</label>
|
|
|
40 <options from_file="pepxml_databases.loc">
|
|
|
41 <column name="name" index="0" />
|
|
|
42 <column name="value" index="2" />
|
|
|
43 </options>
|
|
|
44 </param>
|
|
|
45 </when>
|
|
|
46 <when value="input_ref">
|
|
|
47 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
|
|
|
48 </when>
|
|
|
49 </conditional>
|
|
|
50
|
|
|
51 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
|
|
|
52
|
|
|
53
|
|
|
54 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
|
|
|
55 clicking to select multiple items">
|
|
|
56 <options from_file="tandem_mods.loc">
|
|
|
57 <column name="name" index="0" />
|
|
|
58 <column name="value" index="2" />
|
|
|
59 </options>
|
|
|
60 </param>
|
|
|
61
|
|
|
62 <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).">
|
|
|
63 <param name="custom_mod" type="text">
|
|
|
64 </param>
|
|
|
65 </repeat>
|
|
|
66
|
|
|
67
|
|
|
68 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
|
|
|
69 clicking to select multiple items">
|
|
|
70 <options from_file="tandem_mods.loc">
|
|
|
71 <column name="name" index="0" />
|
|
|
72 <column name="value" index="2" />
|
|
|
73 </options>
|
|
|
74 </param>
|
|
|
75
|
|
|
76 <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).">
|
|
|
77 <param name="custom_mod" type="text">
|
|
|
78 </param>
|
|
|
79 </repeat>
|
|
|
80
|
|
|
81
|
|
|
82
|
|
|
83 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
|
|
|
84 <label>Missed Cleavages Allowed</label>
|
|
|
85 <option value="0">0</option>
|
|
|
86 <option value="1">1</option>
|
|
|
87 <option value="2">2</option>
|
|
|
88 </param>
|
|
|
89
|
|
|
90 <param name="enzyme" type="select" format="text">
|
|
|
91 <label>Enzyme</label>
|
|
|
92 <option value="Trypsin">Trypsin</option>
|
|
|
93 </param>
|
|
|
94
|
|
|
95 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
|
|
|
96
|
|
|
97 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
|
|
|
98 <param name="precursor_tolu" type="select" format="text">
|
|
|
99 <label>Precursor Ion Tolerance Units</label>
|
|
|
100 <option value="ppm">ppm</option>
|
|
|
101 <option value="Da">Da</option>
|
|
|
102 </param>
|
|
|
103
|
|
|
104 <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="--strict-monoisotopic-mass"/>
|
|
|
105
|
|
|
106 </inputs>
|
|
|
107
|
|
|
108
|
|
|
109 <outputs>
|
|
|
110 <data format="raw_pepxml" 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}.pepXML"/>
|
|
|
111 </outputs>
|
|
|
112
|
|
|
113
|
|
|
114 <help>
|
|
|
115
|
|
|
116 **What it does**
|
|
|
117
|
|
|
118 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.
|
|
|
119
|
|
|
120 ----
|
|
|
121
|
|
|
122 **References**
|
|
|
123
|
|
|
124 Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
|
|
|
125
|
|
|
126 </help>
|
|
|
127
|
|
|
128 </tool>
|
