Mercurial > repos > galaxyp > peptideshaker
comparison searchgui.xml @ 44:f35bb9d0c93e draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/peptideshaker commit 981be1bde91d6d565693cd691553f77465e653bb
author | galaxyp |
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date | Tue, 20 Mar 2018 05:09:36 -0400 |
parents | 7963340ab569 |
children | 5fa8b409599e |
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43:7963340ab569 | 44:f35bb9d0c93e |
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1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.3"> | 1 <tool id="search_gui" name="Search GUI" version="@SEARCHGUI_VERSION@.4"> |
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> |
198 -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms} | 198 -andromeda_max_psms ${advanced_options.andromeda.andromeda_max_psms} |
199 -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode} | 199 -andromeda_decoy_mode ${advanced_options.andromeda.andromeda_decoy_mode} |
200 #end if | 200 #end if |
201 *# | 201 *# |
202 | 202 |
203 #* Not working in tests | |
204 #if $advanced_options.tide.tide_advanced == "yes" | 203 #if $advanced_options.tide.tide_advanced == "yes" |
205 -tide_num_ptms ${advanced_options.tide.tide_num_ptms} | 204 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '': |
205 -tide_num_ptms ${advanced_options.tide.tide_max_spectrum_mz} | |
206 #end if | |
206 -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type} | 207 -tide_num_ptms_per_type ${advanced_options.tide.tide_num_ptms_per_type} |
207 -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length} | 208 -tide_min_pep_length ${advanced_options.tide.tide_min_pep_length} |
208 -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length} | 209 -tide_max_pep_length ${advanced_options.tide.tide_max_pep_length} |
209 -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass} | 210 -tide_min_prec_mass ${advanced_options.tide.tide_min_prec_mass} |
210 -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass} | 211 -tide_max_prec_mass ${advanced_options.tide.tide_max_prec_mass} |
211 -tide_decoy_format ${advanced_options.tide.tide_decoy_format} | 212 -tide_decoy_format ${advanced_options.tide.tide_decoy_format} |
212 -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals} | 213 -tide_keep_terminals ${advanced_options.tide.tide_keep_terminals} |
213 | |
214 -tide_output_folder ${advanced_options.tide.tide_output_folder} | |
215 -tide_print_peptides ${advanced_options.tide.tide_print_peptides} | 214 -tide_print_peptides ${advanced_options.tide.tide_print_peptides} |
216 -tide_verbosity ${advanced_options.tide.tide_verbosity} | 215 -tide_verbosity ${advanced_options.tide.tide_verbosity} |
217 -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic} | 216 -tide_monoisotopic ${advanced_options.tide.tide_monoisotopic} |
218 -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term} | 217 -tide_clip_n_term ${advanced_options.tide.tide_clip_n_term} |
219 -tide_digestion_type ${advanced_options.tide.tide_digestion_type} | 218 -tide_digestion_type ${advanced_options.tide.tide_digestion_type} |
220 -tide_compute_sp ${advanced_options.tide.tide_compute_sp} | 219 -tide_compute_sp ${advanced_options.tide.tide_compute_sp} |
221 -tide_max_psms ${advanced_options.tide.tide_max_psms} | 220 -tide_max_psms ${advanced_options.tide.tide_max_psms} |
222 -tide_compute_p ${advanced_options.tide.tide_compute_p} | 221 -tide_compute_p ${advanced_options.tide.tide_compute_p} |
223 -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz} | 222 -tide_min_spectrum_mz ${advanced_options.tide.tide_min_spectrum_mz} |
224 -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz} | 223 #if str($advanced_options.tide.tide_max_spectrum_mz).strip() != '': |
224 -tide_max_spectrum_mz ${advanced_options.tide.tide_max_spectrum_mz} | |
225 #end if | |
225 -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks} | 226 -tide_min_spectrum_peaks ${advanced_options.tide.tide_min_spectrum_peaks} |
226 -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges} | 227 -tide_spectrum_charges ${advanced_options.tide.tide_spectrum_charges} |
227 -tide_remove_prec ${advanced_options.tide.tide_remove_prec} | 228 -tide_remove_prec ${advanced_options.tide.tide_remove_prec} |
228 -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol} | 229 -tide_remove_prec_tol ${advanced_options.tide.tide_remove_prec_tol} |
229 -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator} | 230 -tide_progress_indicator ${advanced_options.tide.tide_progress_indicator} |
230 -tide_use_flanking ${advanced_options.tide.tide_use_flanking} | 231 -tide_use_flanking ${advanced_options.tide.tide_use_flanking} |
231 -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses} | 232 -tide_use_neutral_losses ${advanced_options.tide.tide_use_neutral_losses} |
232 -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width} | 233 -tide_mz_bin_width ${advanced_options.tide.tide_mz_bin_width} |
233 -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset} | 234 -tide_mz_bin_offset ${advanced_options.tide.tide_mz_bin_offset} |
234 -tide_concat ${advanced_options.tide.tide_concat} | 235 -tide_concat ${advanced_options.tide.tide_concat} |
235 -tide_export_text ${advanced_options.tide.tide_export_text} | 236 |
236 -tide_export_sqt ${advanced_options.tide.tide_export_sqt} | 237 #set $formats = ["tide_export_text", "tide_export_sqt", "tide_export_pepxml", "tide_export_mzid", "tide_export_pin"] |
237 -tide_export_pepxml ${advanced_options.tide.tide_export_pepxml} | 238 #for $format in $formats: |
238 -tide_export_mzid ${advanced_options.tide.tide_export_mzid} | 239 #if str($advanced_options.tide.tide_export).strip() == $format: |
239 -tide_export_pin ${advanced_options.tide.tide_export_pin} | 240 -$format 1 |
241 #else: | |
242 -$format 0 | |
243 #end if | |
244 | |
245 #end for | |
246 | |
240 -tide_remove_temp ${advanced_options.tide.tide_remove_temp} | 247 -tide_remove_temp ${advanced_options.tide.tide_remove_temp} |
241 #end if | 248 |
242 *# | 249 #end if |
250 | |
243 | 251 |
244 #if $advanced_options.comet.comet_advanced == "yes" | 252 #if $advanced_options.comet.comet_advanced == "yes" |
245 | 253 |
246 #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes" | 254 #if $advanced_options.comet.comet_spectrum.comet_spectrum_selector == "yes" |
247 -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks} | 255 -comet_min_peaks ${advanced_options.comet.comet_spectrum.comet_min_peaks} |
437 </section> | 445 </section> |
438 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" | 446 <param name="peak_lists" format="mgf" type="data" multiple="true" label="Input Peak Lists (mgf)" |
439 help="Select appropriate MGF dataset(s) from history" /> | 447 help="Select appropriate MGF dataset(s) from history" /> |
440 | 448 |
441 <!-- Search Engine Selection --> | 449 <!-- Search Engine Selection --> |
442 <section name="search_engines_options" expanded="false" title="Search Engine Options"> | 450 <section name="search_engines_options" expanded="true" title="Search Engine Options"> |
443 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> | 451 <param name="engines" type="select" display="checkboxes" multiple="True" label="DB-Search Engines"> |
444 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> | 452 <help>Comet and Tide shouldn't both be selected since they use a similar algoritm.</help> |
445 <option value="X!Tandem" selected="True">X!Tandem</option> | 453 <option value="X!Tandem" selected="True">X!Tandem</option> |
446 | 454 |
447 <option value="MSGF" selected="True">MS-GF+</option> | 455 <option value="MSGF" selected="True">MS-GF+</option> |
448 <option value="OMSSA" selected="True">OMSSA</option> | 456 <option value="OMSSA" selected="True">OMSSA</option> |
449 <option value="Comet">Comet</option> | 457 <option value="Comet">Comet</option> |
450 <!-- Not working in tests | |
451 --> | |
452 <option value="Tide">Tide</option> | 458 <option value="Tide">Tide</option> |
453 <!-- Not working in tests | 459 <!-- Not working in tests |
454 --> | 460 --> |
455 <option value="MyriMatch">MyriMatch</option> | 461 <option value="MyriMatch">MyriMatch</option> |
456 <option value="MS_Amanda">MS_Amanda</option> | 462 <option value="MS_Amanda">MS_Amanda</option> |
746 </when> | 752 </when> |
747 </conditional> | 753 </conditional> |
748 | 754 |
749 | 755 |
750 <!-- TIDE ADVANCED PARAMETERS --> | 756 <!-- TIDE ADVANCED PARAMETERS --> |
751 <!-- Not working in tests | |
752 <conditional name="tide"> | 757 <conditional name="tide"> |
753 <param name="tide_advanced" type="select" label="TIDE Options"> | 758 <param name="tide_advanced" type="select" label="TIDE Options"> |
754 <option value="yes">Advanced</option> | 759 <option value="yes">Advanced</option> |
755 <option value="no" selected="True">Default</option> | 760 <option value="no" selected="True">Default</option> |
756 </param> | 761 </param> |
757 <when value="no" /> | 762 <when value="no" /> |
758 <when value="yes"> | 763 <when value="yes"> |
759 <param name="tide_num_ptms" type="integer" value="100" | 764 <param name="tide_num_ptms" type="integer" value="" optional="true" |
760 label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/> | 765 label="TIDE: Maximum Number of PTMs" help="Set the maximum number of PTMs on peptide to be considered"/> |
761 <param name="tide_num_ptms_per_type" type="integer" value="2" | 766 <param name="tide_num_ptms_per_type" type="integer" value="2" |
762 label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/> | 767 label="TIDE: Maximum Number of PTMs of each Type" help="Set the maximum number of PTMs of each type to be considered"/> |
763 <param name="tide_min_pep_length" type="integer" value="6" | 768 <param name="tide_min_pep_length" type="integer" value="6" |
764 label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/> | 769 label="TIDE: Minimum Peptide Length" help="Set the minimum length of peptide to be considered"/> |
780 <option value="NC" selected="True">NC</option> | 785 <option value="NC" selected="True">NC</option> |
781 <option value="non" >none</option> | 786 <option value="non" >none</option> |
782 </param> | 787 </param> |
783 <param name="tide_decoy_seed" type="integer" value="1" | 788 <param name="tide_decoy_seed" type="integer" value="1" |
784 label="TIDE: Decoy Seed" help="Set the decoy seed"/> | 789 label="TIDE: Decoy Seed" help="Set the decoy seed"/> |
785 <param name="tide_output_folder" type="text" value="crux-output" | |
786 label="TIDE: Output Folder" help="Set the results output folder (relative to the Tide working folder)"/> | |
787 <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false" | 790 <param name="tide_print_peptides" type="boolean" truevalue="1" falsevalue="0" checked="false" |
788 label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/> | 791 label="TIDE: Print Peptides" help="If true, the peptides will be printed in the output"/> |
789 <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress"> | 792 <param name="tide_verbosity" label="TIDE: Progress Display Verbosity" type="select" help="Select the display verbosity level to report the search progress"> |
790 <option value="0" >0</option> | 793 <option value="0" >0</option> |
791 <option value="10" >10</option> | 794 <option value="10" >10</option> |
810 label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/> | 813 label="TIDE: Maximum Number of PSMs" help="Set the maximum number of PSMs to be considered"/> |
811 <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false" | 814 <param name="tide_compute_p" type="boolean" truevalue="1" falsevalue="0" checked="false" |
812 label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/> | 815 label="TIDE: Compute Exact P-value" help="If true, the exact p-values are calculated"/> |
813 <param name="tide_min_spectrum_mz" type="float" value="0.0" | 816 <param name="tide_min_spectrum_mz" type="float" value="0.0" |
814 label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/> | 817 label="TIDE: Minimum Spectrum m/z" help="Set the minimum spectrum m/z value for a spectrum to be considered"/> |
815 <param name="tide_max_spectrum_mz" type="float" value="100000.0" | 818 <param name="tide_max_spectrum_mz" type="float" value="" optional="true" |
816 label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/> | 819 label="TIDE: Maximum Spectrum m/z" help="Set the maximum spectrum m/z value for a spectrum to be considered"/> |
817 <param name="tide_min_spectrum_peaks" type="integer" value="20" | 820 <param name="tide_min_spectrum_peaks" type="integer" value="20" |
818 label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/> | 821 label="TIDE: Minimum Spectrum Peaks" help="Set the minimum amount of peaks in a spectrum for it to be considered"/> |
819 <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching"> | 822 <param name="tide_spectrum_charges" label="TIDE: Spectrum Charges" type="select" help="Select what precursor charges should be taken into account for matching"> |
820 <option value="1" >1</option> | 823 <option value="1" >1</option> |
836 label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/> | 839 label="TIDE: mz Bin Width" help="Choose bin size to analyze the fragmentation spectrum"/> |
837 <param name="tide_mz_bin_offset" type="float" value="0.0" | 840 <param name="tide_mz_bin_offset" type="float" value="0.0" |
838 label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/> | 841 label="TIDE: mz Bin Offset" help="Choose bin offset to analyze the fragmentation spectrum"/> |
839 <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false" | 842 <param name="tide_concat" type="boolean" truevalue="1" falsevalue="0" checked="false" |
840 label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/> | 843 label="TIDE: Concat Target and Decoy" help="If true, the target results are concatenated with the decoy results"/> |
841 <param name="tide_export_text" type="boolean" truevalue="1" falsevalue="0" checked="true" | 844 |
842 label="TIDE: Export Text" help="If true, a text-formatted output file is exported"/> | 845 <param name="tide_export" label="TIDE: Output Format" type="select" help="Choose the output format"> |
843 <param name="tide_export_sqt" type="boolean" truevalue="1" falsevalue="0" checked="false" | 846 <option value="tide_export_text" selected="True">Text</option> |
844 label="TIDE: Export SQT" help="If true, a sqt-formatted output file is exported"/> | 847 <option value="tide_export_sqt" >SQT</option> |
845 <param name="tide_export_pepxml" type="boolean" truevalue="1" falsevalue="0" checked="false" | 848 <option value="tide_export_pepxml" >pepxml</option> |
846 label="TIDE: Export Pepxml" help="If true, a pepxml output file is exported"/> | 849 <!-- |
847 <param name="tide_export_mzid" type="boolean" truevalue="1" falsevalue="0" checked="false" | 850 MZidentML and Percolator input file options generates files with the format (ie. if we use a spectrum file called ´qExactive01819´): |
848 label="TIDE: Export Mzid" help="If true, a mzid output file is exported"/> | 851 galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.target.mzid |
849 <param name="tide_export_pin" type="boolean" truevalue="1" falsevalue="0" checked="false" | 852 instead of |
850 label="TIDE: Export Percolator Input File" help="If true, a percolator input file is exported"/> | 853 galaxy/database/jobs_directory/000/88/working/bin/resources/Tide/linux/linux_64bit/crux-output/qExactive01819.tide-search.mzid |
854 which is the expected one, so current searchgui version gives a "does not exist error". | |
855 --> | |
856 <!-- | |
857 <option value="tide_export_mzid" >MzIdentML</option | |
858 <option value="tide_export_pin" >Percolator input file</option> | |
859 --> | |
860 </param> | |
861 | |
851 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true" | 862 <param name="tide_remove_temp" type="boolean" truevalue="1" falsevalue="0" checked="true" |
852 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/> | 863 label="TIDE: Remove Temp Folders" help="If true, the temp folders are removed when the search is done"/> |
853 </when> | 864 </when> |
854 </conditional> | 865 </conditional> |
855 --> | 866 |
856 | 867 |
857 <!-- MyriMatch ADVANCED PARAMETERS --> | 868 <!-- MyriMatch ADVANCED PARAMETERS --> |
858 <!-- Not working in tests | 869 <!-- Not working in tests |
859 <conditional name="myrimatch"> | 870 <conditional name="myrimatch"> |
860 <param name="myrimatch_advanced" type="select" label="MyriMatch Options"> | 871 <param name="myrimatch_advanced" type="select" label="MyriMatch Options"> |