Mercurial > repos > galaxyp > openms_openswathrtnormalizer
diff OpenSwathRTNormalizer.xml @ 1:580a0a6ab12f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author | galaxyp |
---|---|
date | Tue, 18 Apr 2017 15:46:32 -0400 |
parents | 83818b56fd8c |
children | 13bfce690403 |
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--- a/OpenSwathRTNormalizer.xml Wed Mar 01 09:55:38 2017 -0500 +++ b/OpenSwathRTNormalizer.xml Tue Apr 18 15:46:32 2017 -0400 @@ -65,7 +65,12 @@ -algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_gauss_width #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss: - -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss + -algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss + #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss): + "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss" + #else + $param_algorithm_TransitionGroupPicker_PeakPickerMRM_use_gauss + #end if #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width: -algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width $param_algorithm_TransitionGroupPicker_PeakPickerMRM_peak_width @@ -80,13 +85,23 @@ -algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count $param_algorithm_TransitionGroupPicker_PeakPickerMRM_sn_bin_count #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages: - -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages + -algorithm:TransitionGroupPicker:PeakPickerMRM:write_sn_log_messages + #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages): + "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages" + #else + $param_algorithm_TransitionGroupPicker_PeakPickerMRM_write_sn_log_messages + #end if #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_remove_overlapping_peaks: -algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks #end if #if $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method: - -algorithm:TransitionGroupPicker:PeakPickerMRM:method $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method + -algorithm:TransitionGroupPicker:PeakPickerMRM:method + #if " " in str($param_algorithm_TransitionGroupPicker_PeakPickerMRM_method): + "$param_algorithm_TransitionGroupPicker_PeakPickerMRM_method" + #else + $param_algorithm_TransitionGroupPicker_PeakPickerMRM_method + #end if #end if #if $param_algorithm_DIAScoring_dia_extraction_window: -algorithm:DIAScoring:dia_extraction_window $param_algorithm_DIAScoring_dia_extraction_window @@ -110,7 +125,12 @@ -algorithm:DIAScoring:peak_before_mono_max_ppm_diff $param_algorithm_DIAScoring_peak_before_mono_max_ppm_diff #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 @@ -159,7 +179,12 @@ -algorithm:TransitionGroupPicker:min_peak_width $adv_opts.param_algorithm_TransitionGroupPicker_min_peak_width #end if #if $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction: - -algorithm:TransitionGroupPicker:background_subtraction $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction + -algorithm:TransitionGroupPicker:background_subtraction + #if " " in str($adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction): + "$adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction" + #else + $adv_opts.param_algorithm_TransitionGroupPicker_background_subtraction + #end if #end if #if $adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks: -algorithm:TransitionGroupPicker:recalculate_peaks "$adv_opts.param_algorithm_TransitionGroupPicker_recalculate_peaks" @@ -189,34 +214,84 @@ -algorithm:EMGScoring:statistics:variance $adv_opts.param_algorithm_EMGScoring_statistics_variance #end if #if $adv_opts.param_algorithm_Scores_use_shape_score: - -algorithm:Scores:use_shape_score $adv_opts.param_algorithm_Scores_use_shape_score + -algorithm:Scores:use_shape_score + #if " " in str($adv_opts.param_algorithm_Scores_use_shape_score): + "$adv_opts.param_algorithm_Scores_use_shape_score" + #else + $adv_opts.param_algorithm_Scores_use_shape_score + #end if #end if #if $adv_opts.param_algorithm_Scores_use_coelution_score: - -algorithm:Scores:use_coelution_score $adv_opts.param_algorithm_Scores_use_coelution_score + -algorithm:Scores:use_coelution_score + #if " " in str($adv_opts.param_algorithm_Scores_use_coelution_score): + "$adv_opts.param_algorithm_Scores_use_coelution_score" + #else + $adv_opts.param_algorithm_Scores_use_coelution_score + #end if #end if #if $adv_opts.param_algorithm_Scores_use_rt_score: - -algorithm:Scores:use_rt_score $adv_opts.param_algorithm_Scores_use_rt_score + -algorithm:Scores:use_rt_score + #if " " in str($adv_opts.param_algorithm_Scores_use_rt_score): + "$adv_opts.param_algorithm_Scores_use_rt_score" + #else + $adv_opts.param_algorithm_Scores_use_rt_score + #end if #end if #if $adv_opts.param_algorithm_Scores_use_library_score: - -algorithm:Scores:use_library_score $adv_opts.param_algorithm_Scores_use_library_score + -algorithm:Scores:use_library_score + #if " " in str($adv_opts.param_algorithm_Scores_use_library_score): + "$adv_opts.param_algorithm_Scores_use_library_score" + #else + $adv_opts.param_algorithm_Scores_use_library_score + #end if #end if #if $adv_opts.param_algorithm_Scores_use_elution_model_score: - -algorithm:Scores:use_elution_model_score $adv_opts.param_algorithm_Scores_use_elution_model_score + -algorithm:Scores:use_elution_model_score + #if " " in str($adv_opts.param_algorithm_Scores_use_elution_model_score): + "$adv_opts.param_algorithm_Scores_use_elution_model_score" + #else + $adv_opts.param_algorithm_Scores_use_elution_model_score + #end if #end if #if $adv_opts.param_algorithm_Scores_use_intensity_score: - -algorithm:Scores:use_intensity_score $adv_opts.param_algorithm_Scores_use_intensity_score + -algorithm:Scores:use_intensity_score + #if " " in str($adv_opts.param_algorithm_Scores_use_intensity_score): + "$adv_opts.param_algorithm_Scores_use_intensity_score" + #else + $adv_opts.param_algorithm_Scores_use_intensity_score + #end if #end if #if $adv_opts.param_algorithm_Scores_use_nr_peaks_score: - -algorithm:Scores:use_nr_peaks_score $adv_opts.param_algorithm_Scores_use_nr_peaks_score + -algorithm:Scores:use_nr_peaks_score + #if " " in str($adv_opts.param_algorithm_Scores_use_nr_peaks_score): + "$adv_opts.param_algorithm_Scores_use_nr_peaks_score" + #else + $adv_opts.param_algorithm_Scores_use_nr_peaks_score + #end if #end if #if $adv_opts.param_algorithm_Scores_use_total_xic_score: - -algorithm:Scores:use_total_xic_score $adv_opts.param_algorithm_Scores_use_total_xic_score + -algorithm:Scores:use_total_xic_score + #if " " in str($adv_opts.param_algorithm_Scores_use_total_xic_score): + "$adv_opts.param_algorithm_Scores_use_total_xic_score" + #else + $adv_opts.param_algorithm_Scores_use_total_xic_score + #end if #end if #if $adv_opts.param_algorithm_Scores_use_sn_score: - -algorithm:Scores:use_sn_score $adv_opts.param_algorithm_Scores_use_sn_score + -algorithm:Scores:use_sn_score + #if " " in str($adv_opts.param_algorithm_Scores_use_sn_score): + "$adv_opts.param_algorithm_Scores_use_sn_score" + #else + $adv_opts.param_algorithm_Scores_use_sn_score + #end if #end if #if $adv_opts.param_algorithm_Scores_use_dia_scores: - -algorithm:Scores:use_dia_scores $adv_opts.param_algorithm_Scores_use_dia_scores + -algorithm:Scores:use_dia_scores + #if " " in str($adv_opts.param_algorithm_Scores_use_dia_scores): + "$adv_opts.param_algorithm_Scores_use_dia_scores" + #else + $adv_opts.param_algorithm_Scores_use_dia_scores + #end if #end if #if $adv_opts.param_algorithm_Scores_use_ms1_correlation: -algorithm:Scores:use_ms1_correlation