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comparison tandem.xml @ 0:7fa8d2e2bd3e

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author iracooke
date Wed, 08 May 2013 03:27:27 -0400
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1 <tool id="proteomics_search_tandem_1" name="X!Tandem MSMS Search" version="1.0.1">
2
3 <requirements>
4 <requirement type="package" version="1.2.0">galaxy_protk</requirement>
5 <requirement type="package" version="4.6.1">trans_proteomic_pipeline</requirement>
6 </requirements>
7
8 <description>Run an X!Tandem Search</description>
9
10 <command>
11 #if $database.source_select=="built_in":
12 rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.dbkey
13 #else #rvm 1.9.3@protk-1.2.0 do tandem_search.rb -d $database.fasta_file
14 #end if
15
16 --var-mods='
17 $variable_mods
18 #for $custom_variable_mod in $custom_variable_mods:
19 ,${custom_variable_mod.custom_mod}
20 #end for
21 '
22
23 --fix-mods='
24 $fixed_mods
25 #for $custom_fix_mod in $custom_fix_mods:
26 ,${custom_fix_mod.custom_mod}
27 #end for
28 '
29
30 $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
31
32 </command>
33
34 <inputs>
35 <conditional name="database">
36 <param name="source_select" type="select" label="Database source">
37 <option value="built_in">Built-In</option>
38 <option value="input_ref">Your Upload File</option>
39 </param>
40 <when value="built_in">
41 <param name="dbkey" type="select" format="text" >
42 <label>Database</label>
43 <options from_file="pepxml_databases.loc">
44 <column name="name" index="0" />
45 <column name="value" index="2" />
46 </options>
47 </param>
48 </when>
49 <when value="input_ref">
50 <param name="fasta_file" type="data" format="fasta" label="Uploaded FASTA file" />
51 </when>
52 </conditional>
53
54 <param name="input_file" type="data" format="mzml" multiple="false" label="MSMS File" help="An mzML file with MS/MS data"/>
55
56
57 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
58 clicking to select multiple items">
59 <options from_file="tandem_mods.loc">
60 <column name="name" index="0" />
61 <column name="value" index="2" />
62 </options>
63 </param>
64
65 <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).">
66 <param name="custom_mod" type="text">
67 </param>
68 </repeat>
69
70
71 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
72 clicking to select multiple items">
73 <options from_file="tandem_mods.loc">
74 <column name="name" index="0" />
75 <column name="value" index="2" />
76 </options>
77 </param>
78
79 <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).">
80 <param name="custom_mod" type="text">
81 </param>
82 </repeat>
83
84
85
86 <param name="missed_cleavages" type="select" format="text" help="Allow peptides to contain up to this many missed enzyme cleavage sites">
87 <label>Missed Cleavages Allowed</label>
88 <option value="0">0</option>
89 <option value="1">1</option>
90 <option value="2">2</option>
91 </param>
92
93 <param name="enzyme" type="select" format="text">
94 <label>Enzyme</label>
95 <option value="Trypsin">Trypsin</option>
96 </param>
97
98 <param name="fragment_ion_tol" help="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" label="Fragment ion tolerance"/>
99
100 <param name="precursor_ion_tol" help="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" label="Precursor ion tolerance"/>
101 <param name="precursor_tolu" type="select" format="text">
102 <label>Precursor Ion Tolerance Units</label>
103 <option value="ppm">ppm</option>
104 <option value="Da">Da</option>
105 </param>
106
107 <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"/>
108
109 </inputs>
110
111
112 <outputs>
113 <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"/>
114 </outputs>
115
116 <tests>
117 <test>
118 <param name="source_select" value="input_ref"/>
119 <param name="fasta_file" value="bsa.fasta"/>
120 <param name="input_file" value="bsa.mzML"/>
121 <param name="variable_mods" value="15.994915@M"/>
122 <param name="fixed_mods" value="57.021464@C"/>
123 <param name="allow_multi_isotope_search" value="false"/>
124 <output name="output" file="bsa.pepXML" compare="sim_size" delta="100" />
125 </test>
126 </tests>
127
128
129 <help>
130
131 **What it does**
132
133 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.
134
135 ----
136
137 **References**
138
139 Please see http://www.thegpm.org/GPM/references.html for details of references describing the X!Tandem search engine.
140
141 </help>
142
143 </tool>