Mercurial > repos > iracooke > mascot

comparison mascot.xml @ 10:b3427b77073e draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/iracooke/protk-galaxytools/blob/master/mascot/.shed.yml commit 24e0fef2496984648a8a5cd5bff4d6b9b634a302-dirty
author iracooke
date Tue, 20 Oct 2015 19:50:46 -0400
parents 54c7e3593aac
children
comparison
equal deleted inserted replaced
9:54c7e3593aac 10:b3427b77073e
1 <tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.0"> 1 <tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.1">
2 2 <description>Mascot MS/MS Search</description>
3 <requirements> 3 <requirements>
4 <container type="docker">iracooke/protk-1.4.1</container> 4 <container type="docker">iracooke/protk-1.4.3</container>
5 <requirement type="package" version="1.4">protk</requirement> 5 <requirement type="package" version="1.4.3">protk</requirement>
6 </requirements> 6 </requirements>
7 7 <command>mascot_search.rb
8 <description>Mascot MS/MS Search</description> 8
9 9 #if $database.source_select=="built_in":
10 10 -d $database.dbkey
11 <command>mascot_search.rb 11 #else
12 12 -d $database.custom_db
13 #if $database.source_select=="built_in": 13 #end if
14 -d $database.dbkey 14
15 #else 15 -f $fragment_ion_tol
16 -d $database.custom_db 16 -S $server $input_file
17 #end if 17 -o $output
18 18 -r
19 -f $fragment_ion_tol 19 ## Variable Mods
20 20
21 -S $server $input_file 21 --var-mods='
22 22 $variable_mods
23 -o $output 23 '
24 24 --fix-mods='
25 -r 25 $fixed_mods
26 26 '
27 ## Variable Mods 27
28 28 --allowed-charges='$allowed_charges'
29 --var-mods=' 29 --enzyme=$enzyme
30 $variable_mods 30 --instrument='$instrument'
31 ' 31 -p $precursor_ion_tol
32 32 --precursor-ion-tol-units=$precursor_tolu
33 --fix-mods=' 33
34 $fixed_mods 34 #if $email
35 ' 35 --email=$email
36 36 #end if
37 --allowed-charges='$allowed_charges' 37
38 38 -v $missed_cleavages
39 --enzyme=$enzyme 39
40 40 #if str ( $quant_method ) != 'No Quant'
41 --instrument='$instrument' 41 --quantitation='$quant_method'
42 42 #end if
43 -p $precursor_ion_tol 43
44 44 #if $security.security_use
45 --precursor-ion-tol-units=$precursor_tolu 45 --use-security
46 46 --username $security.username
47 #if $email 47 --password $security.password
48 --email=$email 48 #end if
49 #end if 49
50 50 #if $proxy
51 -v $missed_cleavages 51 --proxy $proxy
52 52 #end if
53 --quantitation='$quant_method' 53
54 54 --timeout=600
55 #if $security.security_use 55
56 --use-security 56 </command>
57 --username $security.username 57 <inputs>
58 --password $security.password 58 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>
59 #end if 59
60 60 <conditional name="database">
61 #if $proxy 61 <param name="source_select" type="select" label="Database Type">
62 --proxy $proxy 62 <option value="built_in">Built-In</option>
63 #end if 63 <option selected="true" value="custom_defined">Custom</option>
64 64 </param>
65 --timeout=600 65 <when value="built_in">
66 66 <param name="dbkey" type="select" format="text" >
67 </command> 67 <label>Database</label>
68 68 <options from_file="mascot_databases.loc">
69 <inputs> 69 <column name="name" index="0" />
70 70 <column name="value" index="2" />
71 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/> 71 </options>
72 72 </param>
73 <conditional name="database"> 73 </when>
74 <param name="source_select" type="select" label="Database Type"> 74 <when value="custom_defined">
75 <option value="built_in">Built-In</option> 75 <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)"/>
76 <option selected="true" value="custom_defined">Custom</option> 76 </when>
77 </param> 77 </conditional>
78 <when value="built_in"> 78
79 <param name="dbkey" type="select" format="text" > 79 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed">
80 <label>Database</label> 80 <options from_file="mascot_mods.loc">
81 <options from_file="mascot_databases.loc"> 81 <column name="name" index="0" />
82 <column name="name" index="0" /> 82 <column name="value" index="2" />
83 <column name="value" index="2" /> 83 </options>
84 </options> 84 </param>
85 </param> 85
86 </when> 86 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed">
87 <when value="custom_defined"> 87 <options from_file="mascot_mods.loc">
88 <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)"/> 88 <column name="name" index="0" />
89 </when> 89 <column name="value" index="2" />
90 </conditional> 90 </options>
91 91 </param>
92 <param name="variable_mods" format="text" type="select" multiple="true" label="Variable Modifications" help="Multiple values allowed"> 92
93 <options from_file="mascot_mods.loc"> 93 <param name="missed_cleavages" type="select" format="text">
94 <column name="name" index="0" /> 94 <label>Missed Cleavages Allowed</label>
95 <column name="value" index="2" /> 95 <option value="0">0</option>
96 </options> 96 <option value="1">1</option>
97 </param> 97 <option selected="true" value="2">2</option>
98 98 </param>
99 <param name="fixed_mods" format="text" type="select" multiple="true" label="Fixed Modifications" help="Multiple values allowed"> 99
100 <options from_file="mascot_mods.loc"> 100 <param name="enzyme" type="select" format="text">
101 <column name="name" index="0" /> 101 <label>Enzyme</label>
102 <column name="value" index="2" /> 102 <option selected="true" value="Trypsin">Trypsin</option>
103 </options> 103 <option value="Trypsin/P">Trypsin/P</option>
104 </param> 104 <option value="Arg-C">Arg-C</option>
105 105 <option value="Asp-N">Asp-N</option>
106 <param name="missed_cleavages" type="select" format="text"> 106 <option value="Asp-N_ambic">Asp-N_ambic</option>
107 <label>Missed Cleavages Allowed</label> 107 <option value="Chymotrypsin">Chymotrypsin</option>
108 <option value="0">0</option> 108 <option value="CNBr">CNBr</option>
109 <option value="1">1</option> 109 <option value="CNBr+Trypsin">CNBr+Trypsin</option>
110 <option selected="true" value="2">2</option> 110 <option value="Formic_acid">Formic_acid</option>
111 </param> 111 <option value="Lys-C">Lys-C</option>
112 112 <option value="Lys-C/P">Lys-C/P</option>
113 <param name="enzyme" type="select" format="text"> 113 <option value="LysC+AspN">LysC+AspN</option>
114 <label>Enzyme</label> 114 <option value="Lys-N">Lys-N</option>
115 <option selected="true" value="Trypsin">Trypsin</option> 115 <option value="PepsinA">PepsinA</option>
116 <option value="Trypsin/P">Trypsin/P</option> 116 <option value="semiTrypsin">semiTrypsin</option>
117 <option value="Arg-C">Arg-C</option> 117 <option value="TrypChymo">TrypChymo</option>
118 <option value="Asp-N">Asp-N</option> 118 <option value="TrypsinMSIPI">TrypsinMSIPI</option>
119 <option value="Asp-N_ambic">Asp-N_ambic</option> 119 <option value="TrypsinMSIPI/P">TrypsinMSIPI/P</option>
120 <option value="Chymotrypsin">Chymotrypsin</option> 120 <option value="V8-DE">V8-DE</option>
121 <option value="CNBr">CNBr</option> 121 <option value="V8-E">V8-E</option>
122 <option value="CNBr+Trypsin">CNBr+Trypsin</option> 122 <option value="none">none</option>
123 <option value="Formic_acid">Formic_acid</option> 123 </param>
124 <option value="Lys-C">Lys-C</option> 124
125 <option value="Lys-C/P">Lys-C/P</option> 125 <param name="allowed_charges" type="select" format="text">
126 <option value="LysC+AspN">LysC+AspN</option> 126 <label>Peptide Charge</label>
127 <option value="Lys-N">Lys-N</option> 127 <option value="8-">8-</option>
128 <option value="PepsinA">PepsinA</option> 128 <option value="7-">7-</option>
129 <option value="semiTrypsin">semiTrypsin</option> 129 <option value="6-">6-</option>
130 <option value="TrypChymo">TrypChymo</option> 130 <option value="5-">5-</option>
131 <option value="TrypsinMSIPI">TrypsinMSIPI</option> 131 <option value="4-">4-</option>
132 <option value="TrypsinMSIPI/P">TrypsinMSIPI/P</option> 132 <option value="3-">3-</option>
133 <option value="V8-DE">V8-DE</option> 133 <option value="2-,3- and 4-">2-,3- and 4-</option>
134 <option value="V8-E">V8-E</option> 134 <option value="2- and 3-">2- and 3-</option>
135 <option value="none">none</option> 135 <option value="2-">2-</option>
136 </param> 136 <option value="1-,2- and 3-">1-,2- and 3-</option>
137 137 <option value="1-">1-</option>
138 <param name="allowed_charges" type="select" format="text"> 138 <option value="Mr">Mr</option>
139 <label>Peptide Charge</label> 139 <option value="1+">1+</option>
140 <option value="8-">8-</option> 140 <option value="1+, 2+ and 3+">1+,2+ and 3+</option>
141 <option value="7-">7-</option> 141 <option value="2+">2+</option>
142 <option value="6-">6-</option> 142 <option value="2+ and 3+">2+ and 3+</option>
143 <option value="5-">5-</option> 143 <option selected="true" value="2+,3+ and 4+">2+,3+ and 4+</option>
144 <option value="4-">4-</option> 144 <option value="3+">3+</option>
145 <option value="3-">3-</option> 145 <option value="4+">4+</option>
146 <option value="2-,3- and 4-">2-,3- and 4-</option> 146 <option value="5+">5+</option>
147 <option value="2- and 3-">2- and 3-</option> 147 <option value="6+">6+</option>
148 <option value="2-">2-</option> 148 <option value="7+">7+</option>
149 <option value="1-,2- and 3-">1-,2- and 3-</option> 149 <option value="8+">8+</option>
150 <option value="1-">1-</option> 150 </param>
151 <option value="Mr">Mr</option> 151
152 <option value="1+">1+</option> 152 <param name="instrument" type="select" format="text">
153 <option value="1+, 2+ and 3+">1+,2+ and 3+</option> 153 <label>Instrument</label>
154 <option value="2+">2+</option> 154 <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
155 <option value="2+ and 3+">2+ and 3+</option> 155 <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
156 <option selected="true" value="2+,3+ and 4+">2+,3+ and 4+</option> 156 <option selected="true" value="ESI-TRAP">ESI-TRAP</option>
157 <option value="3+">3+</option> 157 <option value="ESI-QUAD">ESI-QUAD</option>
158 <option value="4+">4+</option> 158 <option value="ESI-FTICR">ESI-FTICR</option>
159 <option value="5+">5+</option> 159 <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
160 <option value="6+">6+</option> 160 <option value="ESI-4SECTOR">ESI-4SECTOR</option>
161 <option value="7+">7+</option> 161 <option value="FTMS-ECD">FTMS-ECD</option>
162 <option value="8+">8+</option> 162 <option value="ETD-TRAP">ETD-TRAP</option>
163 </param> 163 <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option>
164 164 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
165 <param name="instrument" type="select" format="text"> 165 <option value="MALDI-ISD">MALDI-ISD</option>
166 <label>Instrument</label> 166 <option value="CID+ETD">CID+ETD</option>
167 <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option> 167 </param>
168 <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option> 168
169 <option selected="true" value="ESI-TRAP">ESI-TRAP</option> 169
170 <option value="ESI-QUAD">ESI-QUAD</option> 170 <param name="quant_method" type="select" format="text">
171 <option value="ESI-FTICR">ESI-FTICR</option> 171 <label>Quantitation</label>
172 <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option> 172 <option selected="true" value="No Quant">No Quant</option>
173 <option value="ESI-4SECTOR">ESI-4SECTOR</option> 173 <option value="iTRAQ 4plex">iTRAQ 4plex</option>
174 <option value="FTMS-ECD">FTMS-ECD</option> 174 <option value="iTRAQ 4plex (protein)">iTRAQ 4plex (protein)</option>
175 <option value="ETD-TRAP">ETD-TRAP</option> 175 <option value="iTRAQ 8plex">iTRAQ 8plex</option>
176 <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option> 176 <option value="TMT 6plex">TMT 6plex</option>
177 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option> 177 <option value="TMT 2plex">TMT 2plex</option>
178 <option value="MALDI-ISD">MALDI-ISD</option> 178 <option value="DiLeu 4plex">DiLeu 4plex</option>
179 <option value="CID+ETD">CID+ETD</option> 179 <option value="18O multiplex">18O multiplex</option>
180 </param> 180 <option value="SILAC K+6 R+6 multiplex">SILAC K+6 R+6 multiplex</option>
181 181 <option value="IPTL (Succinyl and IMID) multiplex">IPTL (Succinyl and IMID) multiplex</option>
182 182 <option value="ICPL duplex pre-digest [MD]">ICPL duplex pre-digest [MD]</option>
183 <param name="quant_method" type="select" format="text"> 183 <option value="ICPL duplex post-digest [MD]">ICPL duplex post-digest [MD]</option>
184 <label>Quantitation</label> 184 <option value="ICPL triplex pre-digest [MD]">ICPL triplex pre-digest [MD]</option>
185 <option selected="true" value="None">None</option> 185 <option value="ICPL quadruplex pre-digest [MD]">ICPL quadruplex pre-digest [MD]</option>
186 <option value="iTRAQ 4plex">iTRAQ 4plex</option> 186 <option value="18O corrected [MD]">18O corrected [MD]</option>
187 <option value="iTRAQ 4plex (protein)">iTRAQ 4plex (protein)</option> 187 <option value="15N Metabolic [MD]">15N Metabolic [MD]</option>
188 <option value="iTRAQ 8plex">iTRAQ 8plex</option> 188 <option value="15N + 13C Metabolic [MD]">15N + 13C Metabolic [MD]</option>
189 <option value="TMT 6plex">TMT 6plex</option> 189 <option value="SILAC K+6 R+10 [MD]">SILAC K+6 R+10 [MD]</option>
190 <option value="TMT 2plex">TMT 2plex</option> 190 <option value="SILAC K+6 R+10 Arg-Pro [MD]">SILAC K+6 R+10 Arg-Pro [MD]</option>
191 <option value="DiLeu 4plex">DiLeu 4plex</option> 191 <option value="SILAC K+6 R+6 [MD]">SILAC K+6 R+6 [MD]</option>
192 <option value="18O multiplex">18O multiplex</option> 192 <option value="SILAC R+6 R+10 [MD]">SILAC R+6 R+10 [MD]</option>
193 <option value="SILAC K+6 R+6 multiplex">SILAC K+6 R+6 multiplex</option> 193 <option value="SILAC K+8 R+10 [MD]">SILAC K+8 R+10 [MD]</option>
194 <option value="IPTL (Succinyl and IMID) multiplex">IPTL (Succinyl and IMID) multiplex</option> 194 <option value="SILAC K+4 K+8 R+6 R+10 [MD]">SILAC K+4 K+8 R+6 R+10 [MD]</option>
195 <option value="ICPL duplex pre-digest [MD]">ICPL duplex pre-digest [MD]</option> 195 <option value="ICAT ABI Cleavable [MD]">ICAT ABI Cleavable [MD]</option>
196 <option value="ICPL duplex post-digest [MD]">ICPL duplex post-digest [MD]</option> 196 <option value="ICAT D8 [MD]">ICAT D8 [MD]</option>
197 <option value="ICPL triplex pre-digest [MD]">ICPL triplex pre-digest [MD]</option> 197 <option value="Dimethylation [MD]">Dimethylation [MD]</option>
198 <option value="ICPL quadruplex pre-digest [MD]">ICPL quadruplex pre-digest [MD]</option> 198 <option value="NBS Shimadzu [MD]">NBS Shimadzu [MD]</option>
199 <option value="18O corrected [MD]">18O corrected [MD]</option> 199 <option value="Acetylation [MD]">Acetylation [MD]</option>
200 <option value="15N Metabolic [MD]">15N Metabolic [MD]</option> 200 <option value="Label-free [MD]">Label-free [MD]</option>
201 <option value="15N + 13C Metabolic [MD]">15N + 13C Metabolic [MD]</option> 201 </param>
202 <option value="SILAC K+6 R+10 [MD]">SILAC K+6 R+10 [MD]</option> 202 <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.5" min="0" max="10000" help="Fragment ion tolerance in Daltons"/>
203 <option value="SILAC K+6 R+10 Arg-Pro [MD]">SILAC K+6 R+10 Arg-Pro [MD]</option> 203
204 <option value="SILAC K+6 R+6 [MD]">SILAC K+6 R+6 [MD]</option> 204 <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/>
205 <option value="SILAC R+6 R+10 [MD]">SILAC R+6 R+10 [MD]</option> 205 <param name="precursor_tolu" type="select" format="text">
206 <option value="SILAC K+8 R+10 [MD]">SILAC K+8 R+10 [MD]</option> 206 <label>Precursor Ion Tolerance Units</label>
207 <option value="SILAC K+4 K+8 R+6 R+10 [MD]">SILAC K+4 K+8 R+6 R+10 [MD]</option> 207 <option value="ppm">ppm</option>
208 <option value="ICAT ABI Cleavable [MD]">ICAT ABI Cleavable [MD]</option> 208 <option value="Da">Da</option>
209 <option value="ICAT D8 [MD]">ICAT D8 [MD]</option> 209 </param>
210 <option value="Dimethylation [MD]">Dimethylation [MD]</option> 210
211 <option value="NBS Shimadzu [MD]">NBS Shimadzu [MD]</option> 211 <param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/>
212 <option value="Acetylation [MD]">Acetylation [MD]</option> 212 <param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/>
213 <option value="Label-free [MD]">Label-free [MD]</option> 213
214 </param> 214 <conditional name="security">
215 215 <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" />
216 <param name="fragment_ion_tol" label="Fragment Ion Tolerance" type="float" value="0.5" min="0" max="10000" help="Fragment ion tolerance in Daltons"/> 216 <when value="false" />
217 217 <when value="true">
218 <param name="precursor_ion_tol" label="Precursor Ion Tolerance (Da or ppm)" type="float" value="10" min="0" max="10000" help="Enter a value in Daltons or ppm depending on the units chosen below"/> 218 <param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
219 <param name="precursor_tolu" type="select" format="text"> 219 <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"/>
220 <label>Precursor Ion Tolerance Units</label> 220 </when>
221 <option value="ppm">ppm</option> 221 </conditional>
222 <option value="Da">Da</option> 222 <param name="email" type="text" label="Email " size="60" value="" help=""/>
223 </param> 223 </inputs>
224 224 <outputs>
225 <param name="server" type="text" label="URL to the cgi directory on the Mascot Server " size="60" value="http://www.exampleserver.com/mascot/cgi/"/> 225 <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"/>
226 <param name="proxy" type="text" label="Proxy Server URL including proxy port" size="60" value="" help="eg http://proxy.latrobe.edu.au:8080"/> 226 </outputs>
227 227 <help>
228 <conditional name="security"> 228 Run a Mascot MS/MS Ion Search
229 <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" /> 229 </help>
230 <when value="false" />
231 <when value="true">
232 <param name="username" type="text" label="Username" size="60" value="" help="Username on Mascot Server"/>
233 <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"/>
234 </when>
235 </conditional>
236 <param name="email" type="text" label="Email " size="60" value="" help=""/>
237
238
239
240 </inputs>
241 <outputs>
242 <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"/>
243 </outputs>
244
245 <help>
246 Run a Mascot MS/MS Ion Search
247 </help>
248
249 </tool> 230 </tool>