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comparison mascot.xml @ 8:f567d1818b84 draft

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Docker support and update for protk 1.4
author iracooke
date Thu, 26 Mar 2015 20:04:50 -0400
parents 75184e45bf84
children 54c7e3593aac
comparison
equal deleted inserted replaced
7:75184e45bf84 8:f567d1818b84
1 <tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.0.2"> 1 <tool id="proteomics_search_mascot_1" name="Mascot MSMS Search" version="1.1.0">
2 2
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.3">protk</requirement> 4 <container type="docker">iracooke/protk-1.4.1</container>
5 <requirement type="package" version="1.4">protk</requirement>
5 </requirements> 6 </requirements>
6 7
7 <description>Mascot MS/MS Search</description> 8 <description>Mascot MS/MS Search</description>
8 9
9 10
29 $variable_mods 30 $variable_mods
30 ' 31 '
31 32
32 --fix-mods=' 33 --fix-mods='
33 $fixed_mods 34 $fixed_mods
34 ' 35 '
35 --allowed-charges=$allowed_charges 36
37 --allowed-charges='$allowed_charges'
36 38
37 --enzyme=$enzyme 39 --enzyme=$enzyme
38 40
39 --instrument=$instrument 41 --instrument='$instrument'
40 42
43 -p $precursor_ion_tol
44
41 --precursor-ion-tol-units=$precursor_tolu 45 --precursor-ion-tol-units=$precursor_tolu
42 46
47 #if $email
43 --email=$email 48 --email=$email
49 #end if
44 50
45 -v $missed_cleavages 51 -v $missed_cleavages
52
53 --quantitation='$quant_method'
46 54
47 #if $security.security_use 55 #if $security.security_use
48 --use-security 56 --use-security
49 --username $security.username 57 --username $security.username
50 --password $security.password 58 --password $security.password
52 60
53 #if $proxy 61 #if $proxy
54 --proxy $proxy 62 --proxy $proxy
55 #end if 63 #end if
56 64
65 --timeout=600
66
57 </command> 67 </command>
58 68
59 <inputs> 69 <inputs>
60 70
61 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/> 71 <param name="input_file" type="data" format="mgf" multiple="false" label="MSMS File" help="A Mascot Generic Format file containing MSMS Spectra"/>
62 72
63 <conditional name="database"> 73 <conditional name="database">
64 <param name="source_select" type="select" label="Database Type"> 74 <param name="source_select" type="select" label="Database Type">
65 <option value="built_in">Built-In</option> 75 <option value="built_in">Built-In</option>
66 <option value="custom_defined">Custom</option> 76 <option selected="true" value="custom_defined">Custom</option>
67 </param> 77 </param>
68 <when value="built_in"> 78 <when value="built_in">
69 <param name="dbkey" type="select" format="text" > 79 <param name="dbkey" type="select" format="text" >
70 <label>Database</label> 80 <label>Database</label>
71 <options from_file="mascot_databases.loc"> 81 <options from_file="mascot_databases.loc">
95 105
96 <param name="missed_cleavages" type="select" format="text"> 106 <param name="missed_cleavages" type="select" format="text">
97 <label>Missed Cleavages Allowed</label> 107 <label>Missed Cleavages Allowed</label>
98 <option value="0">0</option> 108 <option value="0">0</option>
99 <option value="1">1</option> 109 <option value="1">1</option>
100 <option value="2">2</option> 110 <option selected="true" value="2">2</option>
101 </param> 111 </param>
102 112
103 <param name="enzyme" type="select" format="text"> 113 <param name="enzyme" type="select" format="text">
104 <label>Enzyme</label> 114 <label>Enzyme</label>
105 <option value="Trypsin">Trypsin</option> 115 <option value="Trypsin">Trypsin</option>
141 <option value="Mr">Mr</option> 151 <option value="Mr">Mr</option>
142 <option value="1+">1+</option> 152 <option value="1+">1+</option>
143 <option value="1+, 2+ and 3+">1+,2+ and 3+</option> 153 <option value="1+, 2+ and 3+">1+,2+ and 3+</option>
144 <option value="2+">2+</option> 154 <option value="2+">2+</option>
145 <option value="2+ and 3+">2+ and 3+</option> 155 <option value="2+ and 3+">2+ and 3+</option>
146 <option value="2+,3+ and 4+">2+,3+ and 4+</option> 156 <option selected="true" value="2+,3+ and 4+">2+,3+ and 4+</option>
147 <option value="3+">3+</option> 157 <option value="3+">3+</option>
148 <option value="4+">4+</option> 158 <option value="4+">4+</option>
149 <option value="5+">5+</option> 159 <option value="5+">5+</option>
150 <option value="6+">6+</option> 160 <option value="6+">6+</option>
151 <option value="7+">7+</option> 161 <option value="7+">7+</option>
154 164
155 <param name="instrument" type="select" format="text"> 165 <param name="instrument" type="select" format="text">
156 <label>Instrument</label> 166 <label>Instrument</label>
157 <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option> 167 <option value="ESI-QUAD-TOF">ESI-QUAD-TOF</option>
158 <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option> 168 <option value="MALDI-TOF-PSD">MALDI-TOF-PSD</option>
159 <option value="ESI-TRAP">ESI-TRAP</option> 169 <option selected="true" value="ESI-TRAP">ESI-TRAP</option>
160 <option value="ESI-QUAD">ESI-QUAD</option> 170 <option value="ESI-QUAD">ESI-QUAD</option>
161 <option value="ESI-FTICR">ESI-FTICR</option> 171 <option value="ESI-FTICR">ESI-FTICR</option>
162 <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option> 172 <option value="MALDI-TOF-TOF">MALDI-TOF-TOF</option>
163 <option value="ESI-4SECTOR">ESI-4SECTOR</option> 173 <option value="ESI-4SECTOR">ESI-4SECTOR</option>
164 <option value="FTMS-ECD">FTMS-ECD</option> 174 <option value="FTMS-ECD">FTMS-ECD</option>
166 <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option> 176 <option value="MALDI-QUAD-TOF">MALDI-QUAD-TOF</option>
167 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option> 177 <option value="MALDI-QIT-TOF">MALDI-QIT-TOF</option>
168 <option value="MALDI-ISD">MALDI-ISD</option> 178 <option value="MALDI-ISD">MALDI-ISD</option>
169 <option value="CID+ETD">CID+ETD</option> 179 <option value="CID+ETD">CID+ETD</option>
170 </param> 180 </param>
171 181
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"/> 182
173 183 <param name="quant_method" type="select" format="text">
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"/> 184 <label>Quantitation</label>
185 <option selected="true" value="None">None</option>
186 <option value="iTRAQ 4plex">iTRAQ 4plex</option>
187 <option value="iTRAQ 4plex (protein)">iTRAQ 4plex (protein)</option>
188 <option value="iTRAQ 8plex">iTRAQ 8plex</option>
189 <option value="TMT 6plex">TMT 6plex</option>
190 <option value="TMT 2plex">TMT 2plex</option>
191 <option value="DiLeu 4plex">DiLeu 4plex</option>
192 <option value="18O multiplex">18O multiplex</option>
193 <option value="SILAC K+6 R+6 multiplex">SILAC K+6 R+6 multiplex</option>
194 <option value="IPTL (Succinyl and IMID) multiplex">IPTL (Succinyl and IMID) multiplex</option>
195 <option value="ICPL duplex pre-digest [MD]">ICPL duplex pre-digest [MD]</option>
196 <option value="ICPL duplex post-digest [MD]">ICPL duplex post-digest [MD]</option>
197 <option value="ICPL triplex pre-digest [MD]">ICPL triplex pre-digest [MD]</option>
198 <option value="ICPL quadruplex pre-digest [MD]">ICPL quadruplex pre-digest [MD]</option>
199 <option value="18O corrected [MD]">18O corrected [MD]</option>
200 <option value="15N Metabolic [MD]">15N Metabolic [MD]</option>
201 <option value="15N + 13C Metabolic [MD]">15N + 13C Metabolic [MD]</option>
202 <option value="SILAC K+6 R+10 [MD]">SILAC K+6 R+10 [MD]</option>
203 <option value="SILAC K+6 R+10 Arg-Pro [MD]">SILAC K+6 R+10 Arg-Pro [MD]</option>
204 <option value="SILAC K+6 R+6 [MD]">SILAC K+6 R+6 [MD]</option>
205 <option value="SILAC R+6 R+10 [MD]">SILAC R+6 R+10 [MD]</option>
206 <option value="SILAC K+8 R+10 [MD]">SILAC K+8 R+10 [MD]</option>
207 <option value="SILAC K+4 K+8 R+6 R+10 [MD]">SILAC K+4 K+8 R+6 R+10 [MD]</option>
208 <option value="ICAT ABI Cleavable [MD]">ICAT ABI Cleavable [MD]</option>
209 <option value="ICAT D8 [MD]">ICAT D8 [MD]</option>
210 <option value="Dimethylation [MD]">Dimethylation [MD]</option>
211 <option value="NBS Shimadzu [MD]">NBS Shimadzu [MD]</option>
212 <option value="Acetylation [MD]">Acetylation [MD]</option>
213 <option value="Label-free [MD]">Label-free [MD]</option>
214 </param>
215
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"/>
217
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"/>
175 <param name="precursor_tolu" type="select" format="text"> 219 <param name="precursor_tolu" type="select" format="text">
176 <label>Precursor Ion Tolerance Units</label> 220 <label>Precursor Ion Tolerance Units</label>
177 <option value="ppm">ppm</option> 221 <option value="ppm">ppm</option>
178 <option value="Da">Da</option> 222 <option value="Da">Da</option>
179 </param> 223 </param>