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comparison IsobaricAnalyzer.xml @ 5:edb972ad2c81 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 58476cadaaf10b494317a604ad81d41c2d15f29b
author galaxyp
date Mon, 12 Feb 2018 12:53:14 -0500
parents 125774c3e8aa
children 7d2ed325f2e5
comparison
equal deleted inserted replaced
4:1dc75c2bf867 5:edb972ad2c81
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 CTDConverter.-->
3 <!--Proposed Tool Section: [Quantitation]--> 3 <!--Proposed Tool Section: [Quantitation]-->
4 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.2.0"> 4 <tool id="IsobaricAnalyzer" name="IsobaricAnalyzer" version="2.3.0">
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>
182 #else 182 #else
183 $token.param_tmt10plex_correction_matrix 183 $token.param_tmt10plex_correction_matrix
184 #end if 184 #end if
185 #end for 185 #end for
186 #end if 186 #end if
187 #if $param_tmt11plex_channel_126_description:
188 -tmt11plex:channel_126_description "$param_tmt11plex_channel_126_description"
189 #end if
190 #if $param_tmt11plex_channel_127N_description:
191 -tmt11plex:channel_127N_description "$param_tmt11plex_channel_127N_description"
192 #end if
193 #if $param_tmt11plex_channel_127C_description:
194 -tmt11plex:channel_127C_description "$param_tmt11plex_channel_127C_description"
195 #end if
196 #if $param_tmt11plex_channel_128N_description:
197 -tmt11plex:channel_128N_description "$param_tmt11plex_channel_128N_description"
198 #end if
199 #if $param_tmt11plex_channel_128C_description:
200 -tmt11plex:channel_128C_description "$param_tmt11plex_channel_128C_description"
201 #end if
202 #if $param_tmt11plex_channel_129N_description:
203 -tmt11plex:channel_129N_description "$param_tmt11plex_channel_129N_description"
204 #end if
205 #if $param_tmt11plex_channel_129C_description:
206 -tmt11plex:channel_129C_description "$param_tmt11plex_channel_129C_description"
207 #end if
208 #if $param_tmt11plex_channel_130N_description:
209 -tmt11plex:channel_130N_description "$param_tmt11plex_channel_130N_description"
210 #end if
211 #if $param_tmt11plex_channel_130C_description:
212 -tmt11plex:channel_130C_description "$param_tmt11plex_channel_130C_description"
213 #end if
214 #if $param_tmt11plex_channel_131N_description:
215 -tmt11plex:channel_131N_description "$param_tmt11plex_channel_131N_description"
216 #end if
217 #if $param_tmt11plex_channel_131C_description:
218 -tmt11plex:channel_131C_description "$param_tmt11plex_channel_131C_description"
219 #end if
220 #if $param_tmt11plex_reference_channel:
221 -tmt11plex:reference_channel
222 #if " " in str($param_tmt11plex_reference_channel):
223 "$param_tmt11plex_reference_channel"
224 #else
225 $param_tmt11plex_reference_channel
226 #end if
227 #end if
228
229 #if $rep_param_tmt11plex_correction_matrix:
230 -tmt11plex:correction_matrix
231 #for token in $rep_param_tmt11plex_correction_matrix:
232 #if " " in str(token):
233 "$token.param_tmt11plex_correction_matrix"
234 #else
235 $token.param_tmt11plex_correction_matrix
236 #end if
237 #end for
238 #end if
187 #if $param_tmt6plex_channel_126_description: 239 #if $param_tmt6plex_channel_126_description:
188 -tmt6plex:channel_126_description "$param_tmt6plex_channel_126_description" 240 -tmt6plex:channel_126_description "$param_tmt6plex_channel_126_description"
189 #end if 241 #end if
190 #if $param_tmt6plex_channel_127_description: 242 #if $param_tmt6plex_channel_127_description:
191 -tmt6plex:channel_127_description "$param_tmt6plex_channel_127_description" 243 -tmt6plex:channel_127_description "$param_tmt6plex_channel_127_description"
232 #end if 284 #end if
233 #end if 285 #end if
234 #end if 286 #end if
235 </command> 287 </command>
236 <inputs> 288 <inputs>
237 <param name="param_type" display="radio" type="select" optional="False" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) "> 289 <param name="param_type" type="select" optional="False" value="itraq4plex" label="Isobaric Quantitation method used in the experiment" help="(-type) ">
238 <option value="itraq4plex" selected="true">itraq4plex</option> 290 <option value="itraq4plex" selected="true">itraq4plex</option>
239 <option value="itraq8plex">itraq8plex</option> 291 <option value="itraq8plex">itraq8plex</option>
240 <option value="tmt10plex">tmt10plex</option> 292 <option value="tmt10plex">tmt10plex</option>
293 <option value="tmt11plex">tmt11plex</option>
241 <option value="tmt6plex">tmt6plex</option> 294 <option value="tmt6plex">tmt6plex</option>
242 </param> 295 </param>
243 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/> 296 <param name="param_in" type="data" format="mzml" optional="False" label="input raw/picked data file" help="(-in) "/>
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)"> 297 <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 share/OpenMS/IDPool/IDPool.txt)">
245 <sanitizer> 298 <sanitizer>
246 <valid initial="string.printable"> 299 <valid initial="string.printable">
247 <remove value="'"/> 300 <remove value="'"/>
248 <remove value="&quot;"/> 301 <remove value="&quot;"/>
249 </valid> 302 </valid>
488 <option value="130C">130C</option> 541 <option value="130C">130C</option>
489 <option value="131">131</option> 542 <option value="131">131</option>
490 </param> 543 </param>
491 <repeat name="rep_param_tmt10plex_correction_matrix" min="0" max="1" title="param_tmt10plex_correction_matrix"> 544 <repeat name="rep_param_tmt10plex_correction_matrix" min="0" max="1" title="param_tmt10plex_correction_matrix">
492 <param name="param_tmt10plex_correction_matrix" type="text" size="30" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'"> 545 <param name="param_tmt10plex_correction_matrix" type="text" size="30" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
546 <sanitizer>
547 <valid initial="string.printable">
548 <remove value="'"/>
549 <remove value="&quot;"/>
550 </valid>
551 </sanitizer>
552 </param>
553 </repeat>
554 <param name="param_tmt11plex_channel_126_description" type="text" size="30" label="Description for the content of the 126 channel" help="(-channel_126_description) ">
555 <sanitizer>
556 <valid initial="string.printable">
557 <remove value="'"/>
558 <remove value="&quot;"/>
559 </valid>
560 </sanitizer>
561 </param>
562 <param name="param_tmt11plex_channel_127N_description" type="text" size="30" label="Description for the content of the 127N channel" help="(-channel_127N_description) ">
563 <sanitizer>
564 <valid initial="string.printable">
565 <remove value="'"/>
566 <remove value="&quot;"/>
567 </valid>
568 </sanitizer>
569 </param>
570 <param name="param_tmt11plex_channel_127C_description" type="text" size="30" label="Description for the content of the 127C channel" help="(-channel_127C_description) ">
571 <sanitizer>
572 <valid initial="string.printable">
573 <remove value="'"/>
574 <remove value="&quot;"/>
575 </valid>
576 </sanitizer>
577 </param>
578 <param name="param_tmt11plex_channel_128N_description" type="text" size="30" label="Description for the content of the 128N channel" help="(-channel_128N_description) ">
579 <sanitizer>
580 <valid initial="string.printable">
581 <remove value="'"/>
582 <remove value="&quot;"/>
583 </valid>
584 </sanitizer>
585 </param>
586 <param name="param_tmt11plex_channel_128C_description" type="text" size="30" label="Description for the content of the 128C channel" help="(-channel_128C_description) ">
587 <sanitizer>
588 <valid initial="string.printable">
589 <remove value="'"/>
590 <remove value="&quot;"/>
591 </valid>
592 </sanitizer>
593 </param>
594 <param name="param_tmt11plex_channel_129N_description" type="text" size="30" label="Description for the content of the 129N channel" help="(-channel_129N_description) ">
595 <sanitizer>
596 <valid initial="string.printable">
597 <remove value="'"/>
598 <remove value="&quot;"/>
599 </valid>
600 </sanitizer>
601 </param>
602 <param name="param_tmt11plex_channel_129C_description" type="text" size="30" label="Description for the content of the 129C channel" help="(-channel_129C_description) ">
603 <sanitizer>
604 <valid initial="string.printable">
605 <remove value="'"/>
606 <remove value="&quot;"/>
607 </valid>
608 </sanitizer>
609 </param>
610 <param name="param_tmt11plex_channel_130N_description" type="text" size="30" label="Description for the content of the 130N channel" help="(-channel_130N_description) ">
611 <sanitizer>
612 <valid initial="string.printable">
613 <remove value="'"/>
614 <remove value="&quot;"/>
615 </valid>
616 </sanitizer>
617 </param>
618 <param name="param_tmt11plex_channel_130C_description" type="text" size="30" label="Description for the content of the 130C channel" help="(-channel_130C_description) ">
619 <sanitizer>
620 <valid initial="string.printable">
621 <remove value="'"/>
622 <remove value="&quot;"/>
623 </valid>
624 </sanitizer>
625 </param>
626 <param name="param_tmt11plex_channel_131N_description" type="text" size="30" label="Description for the content of the 131N channel" help="(-channel_131N_description) ">
627 <sanitizer>
628 <valid initial="string.printable">
629 <remove value="'"/>
630 <remove value="&quot;"/>
631 </valid>
632 </sanitizer>
633 </param>
634 <param name="param_tmt11plex_channel_131C_description" type="text" size="30" label="Description for the content of the 131C channel" help="(-channel_131C_description) ">
635 <sanitizer>
636 <valid initial="string.printable">
637 <remove value="'"/>
638 <remove value="&quot;"/>
639 </valid>
640 </sanitizer>
641 </param>
642 <param name="param_tmt11plex_reference_channel" type="select" optional="False" value="126" label="The reference channel (126, 127N, 127C, 128N, 128C, 129N, 129C, 130N, 130C, 131N, 131C)" help="(-reference_channel) ">
643 <option value="126" selected="true">126</option>
644 <option value="127N">127N</option>
645 <option value="127C">127C</option>
646 <option value="128N">128N</option>
647 <option value="128C">128C</option>
648 <option value="129N">129N</option>
649 <option value="129C">129C</option>
650 <option value="130N">130N</option>
651 <option value="130C">130C</option>
652 <option value="131N">131N</option>
653 <option value="131C">131C</option>
654 </param>
655 <repeat name="rep_param_tmt11plex_correction_matrix" min="0" max="1" title="param_tmt11plex_correction_matrix">
656 <param name="param_tmt11plex_correction_matrix" type="text" size="30" value="0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0 0.0/0.0/0.0/0.0" label="Correction matrix for isotope distributions (see documentation); use the following format: &lt;-2Da&gt;/&lt;-1Da&gt;/&lt;+1Da&gt;/&lt;+2Da&gt;;" help="(-correction_matrix) e.g. '0/0.3/4/0', '0.1/0.3/3/0.2'">
493 <sanitizer> 657 <sanitizer>
494 <valid initial="string.printable"> 658 <valid initial="string.printable">
495 <remove value="'"/> 659 <remove value="'"/>
496 <remove value="&quot;"/> 660 <remove value="&quot;"/>
497 </valid> 661 </valid>