Mercurial > repos > galaxyp > openms_isobaricanalyzer

comparison IsobaricAnalyzer.xml @ 1:125774c3e8aa draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 9a14ed1f2d3c9abdfb080251b3419dd9e0c52a14
author galaxyp
date Wed, 09 Aug 2017 09:05:28 -0400
parents 916f41a35640
children edb972ad2c81
comparison
equal deleted inserted replaced
0:916f41a35640 1:125774c3e8aa
1 <?xml version='1.0' encoding='UTF-8'?> 1 <?xml version='1.0' encoding='UTF-8'?>
2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.--> 2 <!--This is a configuration file for the integration of a tools into Galaxy (https://galaxyproject.org/). This file was automatically generated using CTD2Galaxy.-->
3 <!--Proposed Tool Section: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.1.0"> 4 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.2.0">
5 <description>Calculates isobaric quantitative values for peptides</description> 5 <description>Calculates isobaric quantitative values for peptides</description>
6 <macros> 6 <macros>
7 <token name="@EXECUTABLE@">IsobaricAnalyzer</token> 7 <token name="@EXECUTABLE@">IsobaricAnalyzer</token>
8 <import>macros.xml</import> 8 <import>macros.xml</import>
9 </macros> 9 </macros>
11 <expand macro="stdio"/> 11 <expand macro="stdio"/>
12 <expand macro="requirements"/> 12 <expand macro="requirements"/>
13 <command>IsobaricAnalyzer 13 <command>IsobaricAnalyzer
14 14
15 #if $param_type: 15 #if $param_type:
16 -type $param_type 16 -type
17 #if " " in str($param_type):
18 "$param_type"
19 #else
20 $param_type
21 #end if
17 #end if 22 #end if
18 #if $param_in: 23 #if $param_in:
19 -in $param_in 24 -in $param_in
20 #end if 25 #end if
21 #if $param_out: 26 #if $param_out:
23 #end if 28 #end if
24 #if $param_id_pool: 29 #if $param_id_pool:
25 -id_pool "$param_id_pool" 30 -id_pool "$param_id_pool"
26 #end if 31 #end if
27 #if $param_extraction_select_activation: 32 #if $param_extraction_select_activation:
28 -extraction:select_activation $param_extraction_select_activation 33 -extraction:select_activation
34 #if " " in str($param_extraction_select_activation):
35 "$param_extraction_select_activation"
36 #else
37 $param_extraction_select_activation
38 #end if
29 #end if 39 #end if
30 #if $param_extraction_reporter_mass_shift: 40 #if $param_extraction_reporter_mass_shift:
31 -extraction:reporter_mass_shift $param_extraction_reporter_mass_shift 41 -extraction:reporter_mass_shift $param_extraction_reporter_mass_shift
32 #end if 42 #end if
33 #if $param_extraction_min_precursor_intensity: 43 #if $param_extraction_min_precursor_intensity:
34 -extraction:min_precursor_intensity $param_extraction_min_precursor_intensity 44 -extraction:min_precursor_intensity $param_extraction_min_precursor_intensity
35 #end if 45 #end if
36 #if $param_extraction_keep_unannotated_precursor: 46 #if $param_extraction_keep_unannotated_precursor:
37 -extraction:keep_unannotated_precursor $param_extraction_keep_unannotated_precursor 47 -extraction:keep_unannotated_precursor
48 #if " " in str($param_extraction_keep_unannotated_precursor):
49 "$param_extraction_keep_unannotated_precursor"
50 #else
51 $param_extraction_keep_unannotated_precursor
52 #end if
38 #end if 53 #end if
39 #if $param_extraction_min_reporter_intensity: 54 #if $param_extraction_min_reporter_intensity:
40 -extraction:min_reporter_intensity $param_extraction_min_reporter_intensity 55 -extraction:min_reporter_intensity $param_extraction_min_reporter_intensity
41 #end if 56 #end if
42 #if $param_extraction_discard_low_intensity_quantifications: 57 #if $param_extraction_discard_low_intensity_quantifications:
108 $token.param_itraq8plex_correction_matrix 123 $token.param_itraq8plex_correction_matrix
109 #end if 124 #end if
110 #end for 125 #end for
111 #end if 126 #end if
112 #if $param_quantification_isotope_correction: 127 #if $param_quantification_isotope_correction:
113 -quantification:isotope_correction $param_quantification_isotope_correction 128 -quantification:isotope_correction
129 #if " " in str($param_quantification_isotope_correction):
130 "$param_quantification_isotope_correction"
131 #else
132 $param_quantification_isotope_correction
133 #end if
114 #end if 134 #end if
115 #if $param_quantification_normalization: 135 #if $param_quantification_normalization:
116 -quantification:normalization 136 -quantification:normalization
117 #end if 137 #end if
118 #if $param_tmt10plex_channel_126_description: 138 #if $param_tmt10plex_channel_126_description:
144 #end if 164 #end if
145 #if $param_tmt10plex_channel_131_description: 165 #if $param_tmt10plex_channel_131_description:
146 -tmt10plex:channel_131_description "$param_tmt10plex_channel_131_description" 166 -tmt10plex:channel_131_description "$param_tmt10plex_channel_131_description"
147 #end if 167 #end if
148 #if $param_tmt10plex_reference_channel: 168 #if $param_tmt10plex_reference_channel:
149 -tmt10plex:reference_channel $param_tmt10plex_reference_channel 169 -tmt10plex:reference_channel
170 #if " " in str($param_tmt10plex_reference_channel):
171 "$param_tmt10plex_reference_channel"
172 #else
173 $param_tmt10plex_reference_channel
174 #end if
150 #end if 175 #end if
151 176
152 #if $rep_param_tmt10plex_correction_matrix: 177 #if $rep_param_tmt10plex_correction_matrix:
153 -tmt10plex:correction_matrix 178 -tmt10plex:correction_matrix
154 #for token in $rep_param_tmt10plex_correction_matrix: 179 #for token in $rep_param_tmt10plex_correction_matrix:
197 #end if 222 #end if
198 #if $adv_opts.param_extraction_precursor_isotope_deviation: 223 #if $adv_opts.param_extraction_precursor_isotope_deviation:
199 -extraction:precursor_isotope_deviation $adv_opts.param_extraction_precursor_isotope_deviation 224 -extraction:precursor_isotope_deviation $adv_opts.param_extraction_precursor_isotope_deviation
200 #end if 225 #end if
201 #if $adv_opts.param_extraction_purity_interpolation: 226 #if $adv_opts.param_extraction_purity_interpolation:
202 -extraction:purity_interpolation $adv_opts.param_extraction_purity_interpolation 227 -extraction:purity_interpolation
228 #if " " in str($adv_opts.param_extraction_purity_interpolation):
229 "$adv_opts.param_extraction_purity_interpolation"
230 #else
231 $adv_opts.param_extraction_purity_interpolation
232 #end if
203 #end if 233 #end if
204 #end if 234 #end if
205 </command> 235 </command>
206 <inputs> 236 <inputs>
207 <param name="param_type" display="radio" type="select" optional="False" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) "> 237 <param name="param_type" display="radio" type="select" optional="False" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) ">
209 <option value="itraq8plex">itraq8plex</option> 239 <option value="itraq8plex">itraq8plex</option>
210 <option value="tmt10plex">tmt10plex</option> 240 <option value="tmt10plex">tmt10plex</option>
211 <option value="tmt6plex">tmt6plex</option> 241 <option value="tmt6plex">tmt6plex</option>
212 </param> 242 </param>
213 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/> 243 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
214 <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/miniconda3/envs/py2test/share/OpenMS/IDPool/IDPool.txt)"> 244 <param name="param_id_pool" type="text" size="30" label="ID pool file to DocumentID's for all generated output files" help="(-id_pool) Disabled by default. (Set to 'main' to use /home/ubuntu/mount/miniconda3/envs/openms2.2/share/OpenMS/IDPool/IDPool.txt)">
215 <sanitizer> 245 <sanitizer>
216 <valid initial="string.printable"> 246 <valid initial="string.printable">
217 <remove value="'"/> 247 <remove value="'"/>
218 <remove value="&quot;"/> 248 <remove value="&quot;"/>
219 </valid> 249 </valid>
232 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option> 262 <option value="Low-energy collision-induced dissociation">Low-energy collision-induced dissociation</option>
233 <option value="Photodissociation">Photodissociation</option> 263 <option value="Photodissociation">Photodissociation</option>
234 <option value="Electron transfer dissociation">Electron transfer dissociation</option> 264 <option value="Electron transfer dissociation">Electron transfer dissociation</option>
235 <option value=""></option> 265 <option value=""></option>
236 </param> 266 </param>
237 <param name="param_extraction_reporter_mass_shift" type="float" min="1e-08" max="0.5" optional="True" value="0.1" label="Allowed shift (left to right) in Da from the expected position" help="(-reporter_mass_shift) "/> 267 <param name="param_extraction_reporter_mass_shift" type="float" min="0.0001" max="0.5" optional="True" value="0.002" label="Allowed shift (left to right) in Th from the expected position" help="(-reporter_mass_shift) "/>
238 <param name="param_extraction_min_precursor_intensity" type="float" min="0.0" optional="True" value="1.0" label="Minimum intensity of the precursor to be extracted" help="(-min_precursor_intensity) MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/> 268 <param name="param_extraction_min_precursor_intensity" type="float" min="0.0" optional="True" value="1.0" label="Minimum intensity of the precursor to be extracted" help="(-min_precursor_intensity) MS/MS scans having a precursor with a lower intensity will not be considered for quantitation"/>
239 <param name="param_extraction_keep_unannotated_precursor" display="radio" type="select" optional="False" value="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help="(-keep_unannotated_precursor) "> 269 <param name="param_extraction_keep_unannotated_precursor" display="radio" type="select" optional="False" value="true" label="Flag if precursor with missing intensity value or missing precursor spectrum should be included or not" help="(-keep_unannotated_precursor) ">
240 <option value="true" selected="true">true</option> 270 <option value="true" selected="true">true</option>
241 <option value="false">false</option> 271 <option value="false">false</option>
242 </param> 272 </param>