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comparison searchgui.xml @ 26:3ef5a7dd1a36 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 6dcfe37e286523588aa2738599af8d3273290f28-dirty
author galaxyp
date Tue, 10 May 2016 06:33:08 -0400
parents 815f93bb3e1b
children 432140bcc7fe
comparison
equal deleted inserted replaced
25:0986f68fb410 26:3ef5a7dd1a36
1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.1"> 1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.0">
2 <description> 2 <description>
3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker 3 Perform protein identification using various search engines and prepare results for input to Peptide Shaker
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>macros.xml</import> 6 <import>macros.xml</import>
54 -out SEARCHGUI_IdentificationParameters.par 54 -out SEARCHGUI_IdentificationParameters.par
55 55
56 @GENERAL_PARAMETERS@ 56 @GENERAL_PARAMETERS@
57 57
58 -db input_database.fasta 58 -db input_database.fasta
59 $use_gene_mapping
59 60
60 #if $xtandem.xtandem_advanced == "yes" 61 #if $xtandem.xtandem_advanced == "yes"
61 62
62 -xtandem_npeaks ${xtandem.xtandem_npeaks} 63 -xtandem_npeaks ${xtandem.xtandem_npeaks}
63 -xtandem_min_peaks ${xtandem.xtandem_min_peaks} 64 -xtandem_min_peaks ${xtandem.xtandem_min_peaks}
83 -xtandem_refine_spec_synt ${xtandem.xtandem_refine.xtandem_refine_spec_synt} 84 -xtandem_refine_spec_synt ${xtandem.xtandem_refine.xtandem_refine_spec_synt}
84 -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_pot} 85 -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_pot}
85 -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue} 86 -xtandem_refine_pot ${xtandem.xtandem_refine.xtandem_refine_evalue}
86 87
87 #end if 88 #end if
89 #else
90 -xtandem_output_spectra 1
88 #end if 91 #end if
89 92
90 #if $omssa.omssa_advanced == "yes" 93 #if $omssa.omssa_advanced == "yes"
91 -omssa_hitlist_length ${omssa.hitlist_length} 94 -omssa_hitlist_length ${omssa.hitlist_length}
92 -omssa_remove_prec ${omssa.remove_precursor} 95 -omssa_remove_prec ${omssa.remove_precursor}
141 -msgf_additional ${msgf.msgf_additional} 144 -msgf_additional ${msgf.msgf_additional}
142 -msgf_isotope_low ${msgf.msgf_isotope_low} 145 -msgf_isotope_low ${msgf.msgf_isotope_low}
143 -msgf_isotope_high ${msgf.msgf_isotope_high} 146 -msgf_isotope_high ${msgf.msgf_isotope_high}
144 #end if 147 #end if
145 148
149 #* Not working in tests
146 #if $ms_amanda.ms_amanda_advanced == "yes" 150 #if $ms_amanda.ms_amanda_advanced == "yes"
147 -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy} 151 -ms_amanda_decoy ${ms_amanda.ms_amanda_decoy}
148 -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue} 152 -ms_amanda_max_evalue ${ms_amanda.ms_amanda_max_evalue}
149 -ms_amanda_instrument ${ms_amanda.ms_amanda_instrument} 153 -ms_amanda_instrument ${ms_amanda.ms_amanda_instrument}
150 -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank} 154 -ms_amanda_max_rank ${ms_amanda.ms_amanda_max_rank}
151 -ms_amanda_mono ${ms_amanda.ms_amanda_mono} 155 -ms_amanda_mono ${ms_amanda.ms_amanda_mono}
152 #end if 156 #end if
157 *#
153 158
159 #* Not working in tests
154 #if $myrimatch.myrimatch_advanced == "yes" 160 #if $myrimatch.myrimatch_advanced == "yes"
155 -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length} 161 -myrimatch_min_pep_length ${myrimatch.myrimatch_min_pep_length}
156 -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length} 162 -myrimatch_max_pep_length ${myrimatch.myrimatch_max_pep_length}
157 -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass} 163 -myrimatch_min_prec_mass ${myrimatch.myrimatch_min_prec_mass}
158 -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass} 164 -myrimatch_max_prec_mass ${myrimatch.myrimatch_max_prec_mass}
168 -myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes} 174 -myrimatch_intensity_classes ${myrimatch.myrimatch_intensity_classes}
169 -myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier} 175 -myrimatch_class_multiplier ${myrimatch.myrimatch_class_multiplier}
170 -myrimatch_num_batches ${myrimatch.myrimatch_num_batches} 176 -myrimatch_num_batches ${myrimatch.myrimatch_num_batches}
171 -myrimatch_max_peak ${myrimatch.myrimatch_max_peak} 177 -myrimatch_max_peak ${myrimatch.myrimatch_max_peak}
172 #end if 178 #end if
173 179 *#
174 #* 180
181 #* Not working in tests
175 #if $andromeda.andromeda_advanced == "yes" 182 #if $andromeda.andromeda_advanced == "yes"
176 -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass} 183 -andromeda_max_pep_mass ${andromeda.andromeda_max_pep_mass}
177 -andromeda_max_comb ${andromeda.andromeda_max_comb} 184 -andromeda_max_comb ${andromeda.andromeda_max_comb}
178 -andromeda_top_peaks ${andromeda.andromeda_top_peaks} 185 -andromeda_top_peaks ${andromeda.andromeda_top_peaks}
179 -andromeda_top_peaks_window ${andromeda.andromeda_top_peaks_window} 186 -andromeda_top_peaks_window ${andromeda.andromeda_top_peaks_window}
189 -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length} 196 -andromeda_min_pep_length ${andromeda.andromeda_min_pep_length}
190 -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length} 197 -andromeda_max_pep_length ${andromeda.andromeda_max_pep_length}
191 -andromeda_max_psms ${andromeda.andromeda_max_psms} 198 -andromeda_max_psms ${andromeda.andromeda_max_psms}
192 #end if 199 #end if
193 *# 200 *#
194 201
202 #* Not working in tests
195 #if $tide.tide_advanced == "yes" 203 #if $tide.tide_advanced == "yes"
196 -tide_num_ptms ${tide.tide_num_ptms} 204 -tide_num_ptms ${tide.tide_num_ptms}
197 -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type} 205 -tide_num_ptms_per_type ${tide.tide_num_ptms_per_type}
198 -tide_min_pep_length ${tide.tide_min_pep_length} 206 -tide_min_pep_length ${tide.tide_min_pep_length}
199 -tide_max_pep_length ${tide.tide_max_pep_length} 207 -tide_max_pep_length ${tide.tide_max_pep_length}
228 -tide_export_pepxml ${tide.tide_export_pepxml} 236 -tide_export_pepxml ${tide.tide_export_pepxml}
229 -tide_export_mzid ${tide.tide_export_mzid} 237 -tide_export_mzid ${tide.tide_export_mzid}
230 -tide_export_pin ${tide.tide_export_pin} 238 -tide_export_pin ${tide.tide_export_pin}
231 -tide_remove_temp ${tide.tide_remove_temp} 239 -tide_remove_temp ${tide.tide_remove_temp}
232 #end if 240 #end if
241 *#
233 242
234 #if $comet.comet_advanced == "yes" 243 #if $comet.comet_advanced == "yes"
235 244
236 #if $comet.comet_spectrum.comet_spectrum_selector == "yes" 245 #if $comet.comet_spectrum.comet_spectrum_selector == "yes"
237 -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks} 246 -comet_min_peaks ${comet.comet_spectrum.comet_min_peaks}
291 -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}" 300 -mgf_spectrum_count "${searchgui_advanced.mgf_spectrum_count}"
292 #end if 301 #end if
293 302
294 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created 303 ## Turn of the protein tree generation as it can produce errors if the search is finished before the tree is created
295 ## the tree is generated afterwards in PeptideShaker 304 ## the tree is generated afterwards in PeptideShaker
296 -protein_index 0 305 ## -protein_index 0
297 306
298 ##-makeblastdb_folder \$BLAST_ROOT_DIR 307 ##-makeblastdb_folder \$BLAST_ROOT_DIR
299 308
300 #set $engines_list = str($engines).split(',') 309 #set $engines_list = str($engines).split(',')
301 #if 'X!Tandem' in $engines_list: 310 #if 'X!Tandem' in $engines_list:
358 367
359 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr) 368 (mv output/searchgui_out.zip searchgui_out.zip 2>> $temp_stderr)
360 369
361 && 370 &&
362 371
363 (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr) 372 (zip -u searchgui_out.zip searchgui.properties 2>> $temp_stderr);
364
365 &&
366 373
367 exit_code_for_galaxy=\$?; 374 exit_code_for_galaxy=\$?;
368 cat $temp_stderr 2>&1; 375 cat $temp_stderr 2>&1;
369 (exit \$exit_code_for_galaxy) 376 (exit \$exit_code_for_galaxy)
370 ]]> 377 ]]>
376 383
377 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true" 384 <param name="create_decoy" type="boolean" truevalue="True" falsevalue="False" checked="true"
378 label="Create a concatenated target/decoy database before running PeptideShaker" 385 label="Create a concatenated target/decoy database before running PeptideShaker"
379 help="Selecting this option will help PeptideShaker calculate FDR values" /> 386 help="Selecting this option will help PeptideShaker calculate FDR values" />
380 387
388 <param name="use_gene_mapping" type="boolean" truevalue="-useGeneMapping 1" falsevalue="-useGeneMapping 0" checked="false"
389 label="gene mappings will be used and saved along with the project (UniProt databases only)"
390 help="This should only be enabled for UniProt databaases" />
391
381 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" 392 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)"
382 help="Select appropriate MGF dataset(s) from history" /> 393 help="Select appropriate MGF dataset(s) from history" />
383 394
384 <!-- Search Engine Selection --> 395 <!-- Search Engine Selection -->
385 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> 396 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines">
386 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> 397 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help>
387 <option value="X!Tandem" selected="True">X!Tandem</option> 398 <option value="X!Tandem" selected="True">X!Tandem</option>
388 <option value="MyriMatch">MyriMatch</option> 399 <!-- Not working in tests
389 <option value="MS_Amanda">MS_Amanda</option> 400 <option value="MyriMatch">MyriMatch</option>
401 <option value="MS_Amanda">MS_Amanda</option>
402 -->
390 <option value="MSGF" selected="True">MS-GF+</option> 403 <option value="MSGF" selected="True">MS-GF+</option>
391 <option value="OMSSA" selected="True">OMSSA</option> 404 <option value="OMSSA" selected="True">OMSSA</option>
392 <option value="Comet">Comet</option> 405 <option value="Comet">Comet</option>
406 <!-- Not working in tests
393 <option value="Tide">Tide</option> 407 <option value="Tide">Tide</option>
408 -->
394 <!-- Windows only 409 <!-- Windows only
395 <option value="Andromeda">Andromeda</option> 410 <option value="Andromeda">Andromeda</option>
396 --> 411 -->
397 <validator type="no_options" message="Please select at least one output file" /> 412 <validator type="no_options" message="Please select at least one output file" />
398 </param> 413 </param>
459 <param name="xtandem_output_proteins" help="Controls output of protein sequences" 474 <param name="xtandem_output_proteins" help="Controls output of protein sequences"
460 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" /> 475 label="X!Tandem: Output Proteins" type="boolean" truevalue="1" falsevalue="0" checked="false" />
461 <param name="xtandem_output_sequences" help="Controls output of sequence information" 476 <param name="xtandem_output_sequences" help="Controls output of sequence information"
462 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" /> 477 label="X!Tandem: Output Sequences" type="boolean" truevalue="1" falsevalue="0" checked="false" />
463 <param name="xtandem_output_spectra" help="Controls output of spectrum information" 478 <param name="xtandem_output_spectra" help="Controls output of spectrum information"
464 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="false" /> 479 label="X!Tandem: Output Spectra" type="boolean" truevalue="1" falsevalue="0" checked="true" />
465 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." --> 480 <!-- <param name="xtandem_skyline_path" label="X!Tandem 'spectrum, skyline path'" type="text" help="Path to a spectrum data file for use by skyline." -->
466 481
467 <conditional name="xtandem_refine"><!-- -xtandem_refine --> 482 <conditional name="xtandem_refine"><!-- -xtandem_refine -->
468 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement"> 483 <param name="xtandem_refine_selector" type="select" label="X!Tandem peptide model refinement">
469 <option value="no" selected="True">Don't refine</option> 484 <option value="no" selected="True">Don't refine</option>
640 <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" /> 655 <param name="msgf_isotope_high" label="MSGF: Upper Isotope Error Range" type="integer" value="1" help="Upper isotope errror range" />
641 </when> 656 </when>
642 </conditional> 657 </conditional>
643 658
644 <!-- MS-AMANDA ADVANCED PARAMETERS --> 659 <!-- MS-AMANDA ADVANCED PARAMETERS -->
660 <!-- Not working in tests
645 <conditional name="ms_amanda"> 661 <conditional name="ms_amanda">
646 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options"> 662 <param name="ms_amanda_advanced" type="select" label="MS Amanda Options">
647 <option value="yes">Advanced</option> 663 <option value="yes">Advanced</option>
648 <option value="no" selected="True">Default</option> 664 <option value="no" selected="True">Default</option>
649 </param> 665 </param>
658 label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" /> 674 label="MS Amanda: Maximum Rank" help="MS Amanda maximum rank" />
659 <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true" 675 <param name="ms_amanda_mono" type="boolean" truevalue="1" falsevalue="0" checked="true"
660 label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" /> 676 label="MS Amanda: Use Monoisotopic Mass Values" help="MS Amanda use monoisotopic mass values" />
661 </when> 677 </when>
662 </conditional> 678 </conditional>
679 -->
663 680
664 681
665 <!-- TIDE ADVANCED PARAMETERS --> 682 <!-- TIDE ADVANCED PARAMETERS -->
683 <!-- Not working in tests
666 <conditional name="tide"> 684 <conditional name="tide">
667 <param name="tide_advanced" type="select" label="TIDE Options"> 685 <param name="tide_advanced" type="select" label="TIDE Options">
668 <option value="yes">Advanced</option> 686 <option value="yes">Advanced</option>
669 <option value="no" selected="True">Default</option> 687 <option value="no" selected="True">Default</option>
670 </param> 688 </param>
764 label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/> 782 label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/>
765 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true" 783 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true"
766 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/> 784 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/>
767 </when> 785 </when>
768 </conditional> 786 </conditional>
787 -->
769 788
770 <!-- MyriMatch ADVANCED PARAMETERS --> 789 <!-- MyriMatch ADVANCED PARAMETERS -->
790 <!-- Not working in tests
771 <conditional name="myrimatch"> 791 <conditional name="myrimatch">
772 <param name="myrimatch_advanced" type="select" label="MyriMatch Options"> 792 <param name="myrimatch_advanced" type="select" label="MyriMatch Options">
773 <option value="yes">Advanced</option> 793 <option value="yes">Advanced</option>
774 <option value="no" selected="True">Default</option> 794 <option value="no" selected="True">Default</option>
775 </param> 795 </param>
814 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" /> 834 label="MyriMatch: Number of Batches" help="The number of batches per node to strive for when usinge the MPI-based parallelization features" />
815 <param name="myrimatch_max_peak" type="integer" value="100" 835 <param name="myrimatch_max_peak" type="integer" value="100"
816 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" /> 836 label="MyriMatch: Maximum Peak Count" help="Maximum number of peaks to be used from a spectrum" />
817 </when> 837 </when>
818 </conditional> 838 </conditional>
839 -->
819 840
820 <!-- Andromeda ADVANCED PARAMETERS --> 841 <!-- Andromeda ADVANCED PARAMETERS -->
821 <!-- Windows only 842 <!-- Windows only
822 <conditional name="andromeda"> 843 <conditional name="andromeda">
823 <param name="andromeda_advanced" type="select" label="Andromeda Options"> 844 <param name="andromeda_advanced" type="select" label="Andromeda Options">