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comparison tandem.xml @ 0:b81d7a0466a6

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author iracooke
date Sun, 06 Jan 2013 19:14:28 -0500
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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>