Mercurial > repos > iracooke > mascot

comparison mascot.xml @ 2:579b1f9146b4

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author iracooke
date Mon, 04 Mar 2013 16:28:18 -0500
parents
children d9564913a944
comparison
equal deleted inserted replaced
1:cd2955b6646f 2:579b1f9146b4
1 <tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.0">
2
3
4 <requirements>
5 <requirement type="package" version="1.1.9">galaxy_protk</requirement>
6 </requirements>
7
8 <description>Run a Mascot Search on a File</description>
9
10
11 <command>rvm 1.9.3@protk-1.1.9 do mascot_search.rb -d $database -f $fragment_ion_tol -S $server $input_file -o $output -r
12 ## Variable Mods
13
14 --var-mods='
15 $variable_mods
16 '
17
18 --fix-mods='
19 $fixed_mods
20 '
21 --allowed-charges=$allowed_charges --enzyme=$enzyme --instrument=$instrument --precursor-ion-tol-units=$precursor_tolu --email=$email --username=$username -v $missed_cleavages
22
23 </command>
24
25 <inputs>
26
27 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>
28
29 <param name="database" type="select" format="text" >
30 <label>Database</label>
31 <options from_file="mascot_databases.loc">
32 <column name="name" index="0" />
33 <column name="value" index="2" />
34 </options>
35 </param>
36
37
38
39 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Hold the appropriate key while
40 clicking to select multiple items">
41 <options from_file="mascot_mods.loc">
42 <column name="name" index="0" />
43 <column name="value" index="2" />
44 </options>
45 </param>
46
47 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while
48 clicking to select multiple items">
49 <options from_file="mascot_mods.loc">
50 <column name="name" index="0" />
51 <column name="value" index="2" />
52 </options>
53 </param>
54
55 <param name="missed_cleavages" type="select" format="text">
56 <label>Missed Cleavages Allowed</label>
57 <option value="0">0</option>
58 <option value="1">1</option>
59 <option value="2">2</option>
60 </param>
61
62 <param name="enzyme" type="select" format="text">
63 <label>Enzyme</label>
64 <option value="Trypsin">Trypsin</option>
65 </param>
66
67 <param name="allowed_charges" type="select" format="text">
68 <label>Peptide Charge</label>
69 <option value="8-">8-</option>
70 <option value="7-">7-</option>
71 <option value="6-">6-</option>
72 <option value="5-">5-</option>
73 <option value="4-">4-</option>
74 <option value="3-">3-</option>
75 <option value="2-,3- and 4-">2-,3- and 4-</option>
76 <option value="2- and 3-">2- and 3-</option>
77 <option value="2-">2-</option>
78 <option value="1-,2- and 3-">1-,2- and 3-</option>
79 <option value="1-">1-</option>
80 <option value="Mr">Mr</option>
81 <option value="1+">1+</option>
82 <option value="1+, 2+ and 3+">1+,2+ and 3+</option>
83 <option value="2+">2+</option>
84 <option value="2+ and 3+">2+ and 3+</option>
85 <option value="2+,3+ and 4+">2+,3+ and 4+</option>
86 <option value="3+">3+</option>
87 <option value="4+">4+</option>
88 <option value="5+">5+</option>
89 <option value="6+">6+</option>
90 <option value="7+">7+</option>
91 <option value="8+">8+</option>
92 </param>
93
94 <param name="instrument" type="select" format="text">
95 <label>Instrument</label>
96 <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
97 <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
98 <option value="ESI-TRAP">ESI-TRAP</option>
99 <option value="ESI-QUAD">ESI-QUAD</option>
100 <option value="ESI-FTICR">ESI-FTICR</option>
101 <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
102 <option value="ESI-4SECTOR">ESI-4SECTOR</option>
103 <option value="FTMS-ECD">FTMS-ECD</option>
104 <option value="ETD-TRAP">ETD-TRAP</option>
105 <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option>
106 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
107 <option value="MALDI-ISD">MALDI-ISD</option>
108 <option value="CID+ETD">CID+ETD</option>
109 </param>
110
111 <param name="fragment_ion_tol" label="Fragment Ion Tolerance in Daltons" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
112
113 <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Precursor ion tolerance"/>
114 <param name="precursor_tolu" type="select" format="text">
115 <label>Precursor Ion Tolerance Units</label>
116 <option value="ppm">ppm</option>
117 <option value="Da">Da</option>
118 </param>
119
120 <param name="server" type="text" label="URL to Mascot Server cgi " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
121
122 <param name="email" type="text" label="Email " size="60" value="" help="Not Supported Yet."/>
123
124 <param name="username" type="text" label="Username" size="60" value="" help="Not Supported Yet."/>
125
126 </inputs>
127 <outputs>
128 <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database}.${input_file.display_name}.mascotdat"/>
129 </outputs>
130
131 <help>
132 Run a Mascot Search
133 </help>
134
135 </tool>