Mercurial > repos > galaxyp > openms_openswathanalyzer
changeset 1:7d2394730cdb draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:44:33 -0400 |
| parents | addd804ac6c6 |
| children | 66b3eed59efd |
| files | OpenSwathAnalyzer.xml readme.md |
| diffstat | 2 files changed, 92 insertions(+), 24 deletions(-) [+] |
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--- a/OpenSwathAnalyzer.xml Wed Mar 01 10:20:07 2017 -0500 +++ b/OpenSwathAnalyzer.xml Tue Apr 18 15:44:33 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 @@ -114,7 +129,12 @@ -force #end if #if $adv_opts.param_model_type: - -model:type $adv_opts.param_model_type + -model:type + #if " " in str($adv_opts.param_model_type): + "$adv_opts.param_model_type" + #else + $adv_opts.param_model_type + #end if #end if #if $adv_opts.param_model_symmetric_regression: -model:symmetric_regression @@ -135,7 +155,12 @@ -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" @@ -165,34 +190,84 @@ -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
--- a/readme.md Wed Mar 01 10:20:07 2017 -0500 +++ b/readme.md Tue Apr 18 15:44:33 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.: