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comparison mascot.xml @ 7:75184e45bf84 draft

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author iracooke
date Fri, 13 Jun 2014 18:26:31 -0400
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6:f36b84d1ac09 7:75184e45bf84
1 <tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.2">
2
3 <requirements>
4 <requirement type="package" version="1.3">protk</requirement>
5 </requirements>
6
7 <description>Mascot MS/MS Search</description>
8
9
10 <command>mascot_search.rb
11
12 #if $database.source_select=="built_in":
13 -d $database.dbkey
14 #else
15 -d $database.custom_db
16 #end if
17
18 -f $fragment_ion_tol
19
20 -S $server $input_file
21
22 -o $output
23
24 -r
25
26 ## Variable Mods
27
28 --var-mods='
29 $variable_mods
30 '
31
32 --fix-mods='
33 $fixed_mods
34 '
35 --allowed-charges=$allowed_charges
36
37 --enzyme=$enzyme
38
39 --instrument=$instrument
40
41 --precursor-ion-tol-units=$precursor_tolu
42
43 --email=$email
44
45 -v $missed_cleavages
46
47 #if $security.security_use
48 --use-security
49 --username $security.username
50 --password $security.password
51 #end if
52
53 #if $proxy
54 --proxy $proxy
55 #end if
56
57 </command>
58
59 <inputs>
60
61 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>
62
63 <conditional name="database">
64 <param name="source_select" type="select" label="Database Type">
65 <option value="built_in">Built-In</option>
66 <option value="custom_defined">Custom</option>
67 </param>
68 <when value="built_in">
69 <param name="dbkey" type="select" format="text" >
70 <label>Database</label>
71 <options from_file="mascot_databases.loc">
72 <column name="name" index="0" />
73 <column name="value" index="2" />
74 </options>
75 </param>
76 </when>
77 <when value="custom_defined">
78 <param name="custom_db" type="text" size="80" value="SwissProt" label="Database Name" help="Exact name of a database defined on the Mascot server (case-sensitive)"/>
79 </when>
80 </conditional>
81
82 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">
83 <options from_file="mascot_mods.loc">
84 <column name="name" index="0" />
85 <column name="value" index="2" />
86 </options>
87 </param>
88
89 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">
90 <options from_file="mascot_mods.loc">
91 <column name="name" index="0" />
92 <column name="value" index="2" />
93 </options>
94 </param>
95
96 <param name="missed_cleavages" type="select" format="text">
97 <label>Missed Cleavages Allowed</label>
98 <option value="0">0</option>
99 <option value="1">1</option>
100 <option value="2">2</option>
101 </param>
102
103 <param name="enzyme" type="select" format="text">
104 <label>Enzyme</label>
105 <option value="Trypsin">Trypsin</option>
106 <option value="Trypsin/P">Trypsin/P</option>
107 <option value="Arg-C">Arg-C</option>
108 <option value="Asp-N">Asp-N</option>
109 <option value="Asp-N_ambic">Asp-N_ambic</option>
110 <option value="Chymotrypsin">Chymotrypsin</option>
111 <option value="CNBr">CNBr</option>
112 <option value="CNBr+Trypsin">CNBr+Trypsin</option>
113 <option value="Formic_acid">Formic_acid</option>
114 <option value="Lys-C">Lys-C</option>
115 <option value="Lys-C/P">Lys-C/P</option>
116 <option value="LysC+AspN">LysC+AspN</option>
117 <option value="Lys-N">Lys-N</option>
118 <option value="PepsinA">PepsinA</option>
119 <option value="semiTrypsin">semiTrypsin</option>
120 <option value="TrypChymo">TrypChymo</option>
121 <option value="TrypsinMSIPI">TrypsinMSIPI</option>
122 <option value="TrypsinMSIPI/P">TrypsinMSIPI/P</option>
123 <option value="V8-DE">V8-DE</option>
124 <option value="V8-E">V8-E</option>
125 <option value="none">none</option>
126 </param>
127
128 <param name="allowed_charges" type="select" format="text">
129 <label>Peptide Charge</label>
130 <option value="8-">8-</option>
131 <option value="7-">7-</option>
132 <option value="6-">6-</option>
133 <option value="5-">5-</option>
134 <option value="4-">4-</option>
135 <option value="3-">3-</option>
136 <option value="2-,3- and 4-">2-,3- and 4-</option>
137 <option value="2- and 3-">2- and 3-</option>
138 <option value="2-">2-</option>
139 <option value="1-,2- and 3-">1-,2- and 3-</option>
140 <option value="1-">1-</option>
141 <option value="Mr">Mr</option>
142 <option value="1+">1+</option>
143 <option value="1+, 2+ and 3+">1+,2+ and 3+</option>
144 <option value="2+">2+</option>
145 <option value="2+ and 3+">2+ and 3+</option>
146 <option value="2+,3+ and 4+">2+,3+ and 4+</option>
147 <option value="3+">3+</option>
148 <option value="4+">4+</option>
149 <option value="5+">5+</option>
150 <option value="6+">6+</option>
151 <option value="7+">7+</option>
152 <option value="8+">8+</option>
153 </param>
154
155 <param name="instrument" type="select" format="text">
156 <label>Instrument</label>
157 <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
158 <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
159 <option value="ESI-TRAP">ESI-TRAP</option>
160 <option value="ESI-QUAD">ESI-QUAD</option>
161 <option value="ESI-FTICR">ESI-FTICR</option>
162 <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
163 <option value="ESI-4SECTOR">ESI-4SECTOR</option>
164 <option value="FTMS-ECD">FTMS-ECD</option>
165 <option value="ETD-TRAP">ETD-TRAP</option>
166 <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option>
167 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
168 <option value="MALDI-ISD">MALDI-ISD</option>
169 <option value="CID+ETD">CID+ETD</option>
170 </param>
171
172 <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
173
174 <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="100" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>
175 <param name="precursor_tolu" type="select" format="text">
176 <label>Precursor Ion Tolerance Units</label>
177 <option value="ppm">ppm</option>
178 <option value="Da">Da</option>
179 </param>
180
181 <param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
182 <param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/>
183
184 <conditional name="security">
185 <param name="security_use" type="boolean" label="Use Mascot Security?" help="Select this if you need to enter a username and password" truevalue="true" falsevalue="false" />
186 <when value="false" />
187 <when value="true">
188 <param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
189 <param name="password" type="text" label="Password" size="60" value="" help="Mascot Password. Password is encrypted when over the internet but is stored in clear-text on the Galaxy server"/>
190 </when>
191 </conditional>
192 <param name="email" type="text" label="Email " size="60" value="" help=""/>
193
194
195
196 </inputs>
197 <outputs>
198 <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database.dbkey if $database.has_key('dbkey') else $database.custom_db}.${input_file.display_name}.mascotdat"/>
199 </outputs>
200
201 <help>
202 Run a Mascot MS/MS Ion Search
203 </help>
204
205 </tool>