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comparison mascot.xml @ 5:327b2d99d4c5

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Update
author Ira Cooke <iracooke@gmail.com>
date Sun, 09 Jun 2013 08:17:38 -0500
parents d9564913a944
children
comparison
equal deleted inserted replaced
4:d9564913a944 5:327b2d99d4c5
1 <tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.1"> 1 <tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.1">
2 2
3 3
4 <requirements> 4 <requirements>
5 <requirement type="package" version="1.2.0">galaxy_protk</requirement> 5 <requirement type="package" version="1.2.2">galaxy_protk</requirement>
6 </requirements> 6 </requirements>
7 7
8 <description>Mascot MS/MS Search</description> 8 <description>Mascot MS/MS Search</description>
9 9
10 10
11 <command>rvm 1.9.3@protk-1.2.0 do mascot_search.rb -d $database -f $fragment_ion_tol -S $server $input_file -o $output -r 11 <command>rvm 1.9.3@protk-1.2.2 do mascot_search.rb
12
13 #if $database.source_select=="built_in":
14 -d $database.dbkey
15 #else
16 -d $database.custom_db
17 #end if
18
19 -f $fragment_ion_tol
20
21 -S $server $input_file
22
23 -o $output
24
25 -r
26
12 ## Variable Mods 27 ## Variable Mods
13 28
14 --var-mods=' 29 --var-mods='
15 $variable_mods 30 $variable_mods
16 ' 31 '
17 32
18 --fix-mods=' 33 --fix-mods='
19 $fixed_mods 34 $fixed_mods
20 ' 35 '
21 --allowed-charges=$allowed_charges --enzyme=$enzyme --instrument=$instrument --precursor-ion-tol-units=$precursor_tolu --email=$email --username=$username -v $missed_cleavages 36 --allowed-charges=$allowed_charges
22 37
38 --enzyme=$enzyme
39
40 --instrument=$instrument
41
42 --precursor-ion-tol-units=$precursor_tolu
43
44 --email=$email
45
46 -v $missed_cleavages
47
48 #if $security.security_use
49 --use-security
50 --username $security.username
51 --password $security.password
52 #end if
53
54 #if $proxy
55 --proxy $proxy
56 #end if
57
23 </command> 58 </command>
24 59
25 <inputs> 60 <inputs>
26 61
27 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/> 62 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>
28 63
29 <param name="database" type="select" format="text" > 64 <conditional name="database">
30 <label>Database</label> 65 <param name="source_select" type="select" label="Database Type">
31 <options from_file="mascot_databases.loc"> 66 <option value="built_in">Built-In</option>
32 <column name="name" index="0" /> 67 <option value="custom_defined">Custom</option>
33 <column name="value" index="2" /> 68 </param>
34 </options> 69 <when value="built_in">
35 </param> 70 <param name="dbkey" type="select" format="text" >
71 <label>Database</label>
72 <options from_file="mascot_databases.loc">
73 <column name="name" index="0" />
74 <column name="value" index="2" />
75 </options>
76 </param>
77 </when>
78 <when value="custom_defined">
79 <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)"/>
80 </when>
81 </conditional>
36 82
37 83 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">
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"> 84 <options from_file="mascot_mods.loc">
42 <column name="name" index="0" /> 85 <column name="name" index="0" />
43 <column name="value" index="2" /> 86 <column name="value" index="2" />
44 </options> 87 </options>
45 </param> 88 </param>
46 89
47 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Hold the appropriate key while 90 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">
48 clicking to select multiple items">
49 <options from_file="mascot_mods.loc"> 91 <options from_file="mascot_mods.loc">
50 <column name="name" index="0" /> 92 <column name="name" index="0" />
51 <column name="value" index="2" /> 93 <column name="value" index="2" />
52 </options> 94 </options>
53 </param> 95 </param>
106 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option> 148 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
107 <option value="MALDI-ISD">MALDI-ISD</option> 149 <option value="MALDI-ISD">MALDI-ISD</option>
108 <option value="CID+ETD">CID+ETD</option> 150 <option value="CID+ETD">CID+ETD</option>
109 </param> 151 </param>
110 152
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"/> 153 <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.65" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
112 154
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"/> 155 <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"/>
114 <param name="precursor_tolu" type="select" format="text"> 156 <param name="precursor_tolu" type="select" format="text">
115 <label>Precursor Ion Tolerance Units</label> 157 <label>Precursor Ion Tolerance Units</label>
116 <option value="ppm">ppm</option> 158 <option value="ppm">ppm</option>
117 <option value="Da">Da</option> 159 <option value="Da">Da</option>
118 </param> 160 </param>
119 161
120 <param name="server" type="text" label="URL to Mascot Server cgi " size="60" value="http://www.exampleserver.com/mascot/cgi/"/> 162 <param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
163 <param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/>
164
165 <conditional name="security">
166 <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" />
167 <when value="false" />
168 <when value="true">
169 <param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
170 <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"/>
171 </when>
172 </conditional>
173 <param name="email" type="text" label="Email " size="60" value="" help=""/>
121 174
122 <param name="email" type="text" label="Email " size="60" value="" help="Not Supported Yet."/>
123 175
124 <param name="username" type="text" label="Username" size="60" value="" help="Not Supported Yet."/>
125 176
126 </inputs> 177 </inputs>
127 <outputs> 178 <outputs>
128 <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database}.${input_file.display_name}.mascotdat"/> 179 <data format="mascotdat" name="output" metadata_source="input_file" label="mascot_vs_${database.dbkey if $database.has_key('dbkey') else $database.custom_db}.${input_file.display_name}.mascotdat"/>
129 </outputs> 180 </outputs>
130 181
131 <help> 182 <help>
132 Run a Mascot Search 183 Run a Mascot Search
133 </help> 184 </help>