Mercurial > repos > galaxyp > openms_openswathworkflow
changeset 1:34479f097d1b draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:46:58 -0400 |
| parents | 99766e796721 |
| children | a46df1a24002 |
| files | OpenSwathWorkflow.xml readme.md |
| diffstat | 2 files changed, 98 insertions(+), 25 deletions(-) [+] |
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--- a/OpenSwathWorkflow.xml Wed Mar 01 10:17:37 2017 -0500 +++ b/OpenSwathWorkflow.xml Tue Apr 18 15:46:58 2017 -0400 @@ -67,7 +67,12 @@ -Scoring:TransitionGroupPicker:min_peak_width $param_Scoring_TransitionGroupPicker_min_peak_width #end if #if $param_Scoring_TransitionGroupPicker_background_subtraction: - -Scoring:TransitionGroupPicker:background_subtraction $param_Scoring_TransitionGroupPicker_background_subtraction + -Scoring:TransitionGroupPicker:background_subtraction + #if " " in str($param_Scoring_TransitionGroupPicker_background_subtraction): + "$param_Scoring_TransitionGroupPicker_background_subtraction" + #else + $param_Scoring_TransitionGroupPicker_background_subtraction + #end if #end if #if $param_Scoring_TransitionGroupPicker_recalculate_peaks: -Scoring:TransitionGroupPicker:recalculate_peaks "$param_Scoring_TransitionGroupPicker_recalculate_peaks" @@ -103,10 +108,20 @@ -Scoring:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages #end if #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks: - -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks + -Scoring:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks + #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks): + "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks" + #else + $param_Scoring_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks + #end if #end if #if $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method: - -Scoring:TransitionGroupPicker:PeakPickerMRM:method $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method + -Scoring:TransitionGroupPicker:PeakPickerMRM:method + #if " " in str($param_Scoring_TransitionGroupPicker_PeakPickerMRM_method): + "$param_Scoring_TransitionGroupPicker_PeakPickerMRM_method" + #else + $param_Scoring_TransitionGroupPicker_PeakPickerMRM_method + #end if #end if #if $param_Scoring_DIAScoring_dia_extraction_window: -Scoring:DIAScoring:dia_extraction_window $param_Scoring_DIAScoring_dia_extraction_window @@ -133,7 +148,12 @@ -Scoring:EMGScoring:max_iteration $param_Scoring_EMGScoring_max_iteration #end if #if $param_outlierDetection_outlierMethod: - -outlierDetection:outlierMethod $param_outlierDetection_outlierMethod + -outlierDetection:outlierMethod + #if " " in str($param_outlierDetection_outlierMethod): + "$param_outlierDetection_outlierMethod" + #else + $param_outlierDetection_outlierMethod + #end if #end if #if $param_outlierDetection_useIterativeChauvenet: -outlierDetection:useIterativeChauvenet @@ -200,16 +220,31 @@ -use_elution_model_score #end if #if $adv_opts.param_readOptions: - -readOptions $adv_opts.param_readOptions + -readOptions + #if " " in str($adv_opts.param_readOptions): + "$adv_opts.param_readOptions" + #else + $adv_opts.param_readOptions + #end if #end if #if $adv_opts.param_mz_correction_function: - -mz_correction_function $adv_opts.param_mz_correction_function + -mz_correction_function + #if " " in str($adv_opts.param_mz_correction_function): + "$adv_opts.param_mz_correction_function" + #else + $adv_opts.param_mz_correction_function + #end if #end if #if $adv_opts.param_tempDirectory: -tempDirectory "$adv_opts.param_tempDirectory" #end if #if $adv_opts.param_extraction_function: - -extraction_function $adv_opts.param_extraction_function + -extraction_function + #if " " in str($adv_opts.param_extraction_function): + "$adv_opts.param_extraction_function" + #else + $adv_opts.param_extraction_function + #end if #end if #if $adv_opts.param_batchSize: -batchSize $adv_opts.param_batchSize @@ -224,31 +259,76 @@ -Scoring:write_convex_hull #end if #if $adv_opts.param_Scoring_Scores_use_shape_score: - -Scoring:Scores:use_shape_score $adv_opts.param_Scoring_Scores_use_shape_score + -Scoring:Scores:use_shape_score + #if " " in str($adv_opts.param_Scoring_Scores_use_shape_score): + "$adv_opts.param_Scoring_Scores_use_shape_score" + #else + $adv_opts.param_Scoring_Scores_use_shape_score + #end if #end if #if $adv_opts.param_Scoring_Scores_use_coelution_score: - -Scoring:Scores:use_coelution_score $adv_opts.param_Scoring_Scores_use_coelution_score + -Scoring:Scores:use_coelution_score + #if " " in str($adv_opts.param_Scoring_Scores_use_coelution_score): + "$adv_opts.param_Scoring_Scores_use_coelution_score" + #else + $adv_opts.param_Scoring_Scores_use_coelution_score + #end if #end if #if $adv_opts.param_Scoring_Scores_use_rt_score: - -Scoring:Scores:use_rt_score $adv_opts.param_Scoring_Scores_use_rt_score + -Scoring:Scores:use_rt_score + #if " " in str($adv_opts.param_Scoring_Scores_use_rt_score): + "$adv_opts.param_Scoring_Scores_use_rt_score" + #else + $adv_opts.param_Scoring_Scores_use_rt_score + #end if #end if #if $adv_opts.param_Scoring_Scores_use_library_score: - -Scoring:Scores:use_library_score $adv_opts.param_Scoring_Scores_use_library_score + -Scoring:Scores:use_library_score + #if " " in str($adv_opts.param_Scoring_Scores_use_library_score): + "$adv_opts.param_Scoring_Scores_use_library_score" + #else + $adv_opts.param_Scoring_Scores_use_library_score + #end if #end if #if $adv_opts.param_Scoring_Scores_use_intensity_score: - -Scoring:Scores:use_intensity_score $adv_opts.param_Scoring_Scores_use_intensity_score + -Scoring:Scores:use_intensity_score + #if " " in str($adv_opts.param_Scoring_Scores_use_intensity_score): + "$adv_opts.param_Scoring_Scores_use_intensity_score" + #else + $adv_opts.param_Scoring_Scores_use_intensity_score + #end if #end if #if $adv_opts.param_Scoring_Scores_use_nr_peaks_score: - -Scoring:Scores:use_nr_peaks_score $adv_opts.param_Scoring_Scores_use_nr_peaks_score + -Scoring:Scores:use_nr_peaks_score + #if " " in str($adv_opts.param_Scoring_Scores_use_nr_peaks_score): + "$adv_opts.param_Scoring_Scores_use_nr_peaks_score" + #else + $adv_opts.param_Scoring_Scores_use_nr_peaks_score + #end if #end if #if $adv_opts.param_Scoring_Scores_use_total_xic_score: - -Scoring:Scores:use_total_xic_score $adv_opts.param_Scoring_Scores_use_total_xic_score + -Scoring:Scores:use_total_xic_score + #if " " in str($adv_opts.param_Scoring_Scores_use_total_xic_score): + "$adv_opts.param_Scoring_Scores_use_total_xic_score" + #else + $adv_opts.param_Scoring_Scores_use_total_xic_score + #end if #end if #if $adv_opts.param_Scoring_Scores_use_sn_score: - -Scoring:Scores:use_sn_score $adv_opts.param_Scoring_Scores_use_sn_score + -Scoring:Scores:use_sn_score + #if " " in str($adv_opts.param_Scoring_Scores_use_sn_score): + "$adv_opts.param_Scoring_Scores_use_sn_score" + #else + $adv_opts.param_Scoring_Scores_use_sn_score + #end if #end if #if $adv_opts.param_Scoring_Scores_use_dia_scores: - -Scoring:Scores:use_dia_scores $adv_opts.param_Scoring_Scores_use_dia_scores + -Scoring:Scores:use_dia_scores + #if " " in str($adv_opts.param_Scoring_Scores_use_dia_scores): + "$adv_opts.param_Scoring_Scores_use_dia_scores" + #else + $adv_opts.param_Scoring_Scores_use_dia_scores + #end if #end if #if $adv_opts.param_Scoring_Scores_use_ms1_correlation: -Scoring:Scores:use_ms1_correlation
--- a/readme.md Wed Mar 01 10:17:37 2017 -0500 +++ b/readme.md Tue Apr 18 15:46:58 2017 -0400 @@ -39,10 +39,10 @@ * clone or install CTD2Galaxy ```bash - git clone https://github.com/blankclemens/CTD2Galaxy.git + git clone https://github.com/WorkflowConversion/CTD2Galaxy.git ``` - * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. + * If you have CTDopts and CTD2Galaxy installed you are ready to generate Galaxy Tools from CTD definitions. Change the following command according to your needs, especially the `/PATH/TO` parts. The default files are provided in this repository. ```bash python generator.py \ @@ -102,13 +102,6 @@ [...] ]]> ``` - * In `PeakPickerHiRes.xml`, the parameter `report_FWHM_unit` has to be put in quotation marks. Look for the following line - - -algorithm:report_FWHM_unit $param_algorithm_report_FWHM_unit - - and change it to - - -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit" * In `FileConverter.xml` add `auto_format="true"` to the output, e.g.: