Mercurial > repos > galaxyp > openms_precursorionselector
changeset 1:ba0c07f3cb9f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:48:45 -0400 |
| parents | d53ccfc9c11f |
| children | ea4d633cc76d |
| files | PrecursorIonSelector.xml readme.md |
| diffstat | 2 files changed, 26 insertions(+), 13 deletions(-) [+] |
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--- a/PrecursorIonSelector.xml Wed Mar 01 09:57:53 2017 -0500 +++ b/PrecursorIonSelector.xml Tue Apr 18 15:48:45 2017 -0400 @@ -63,7 +63,12 @@ #end for #end if #if $param_algorithm_type: - -algorithm:type $param_algorithm_type + -algorithm:type + #if " " in str($param_algorithm_type): + "$param_algorithm_type" + #else + $param_algorithm_type + #end if #end if #if $param_algorithm_max_iteration: -algorithm:max_iteration $param_algorithm_max_iteration @@ -120,7 +125,12 @@ -algorithm:MIPFormulation:combined_ilp:k3 $param_algorithm_MIPFormulation_combined_ilp_k3 #end if #if $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs: - -algorithm:MIPFormulation:combined_ilp:scale_matching_probs $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs + -algorithm:MIPFormulation:combined_ilp:scale_matching_probs + #if " " in str($param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs): + "$param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs" + #else + $param_algorithm_MIPFormulation_combined_ilp_scale_matching_probs + #end if #end if #if $param_algorithm_MIPFormulation_feature_based_no_intensity_normalization: -algorithm:MIPFormulation:feature_based:no_intensity_normalization @@ -132,7 +142,12 @@ -algorithm:Preprocessing:precursor_mass_tolerance $param_algorithm_Preprocessing_precursor_mass_tolerance #end if #if $param_algorithm_Preprocessing_precursor_mass_tolerance_unit: - -algorithm:Preprocessing:precursor_mass_tolerance_unit $param_algorithm_Preprocessing_precursor_mass_tolerance_unit + -algorithm:Preprocessing:precursor_mass_tolerance_unit + #if " " in str($param_algorithm_Preprocessing_precursor_mass_tolerance_unit): + "$param_algorithm_Preprocessing_precursor_mass_tolerance_unit" + #else + $param_algorithm_Preprocessing_precursor_mass_tolerance_unit + #end if #end if #if $param_algorithm_Preprocessing_preprocessed_db_path: -algorithm:Preprocessing:preprocessed_db_path "$param_algorithm_Preprocessing_preprocessed_db_path" @@ -175,7 +190,12 @@ #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_solver: - -solver $adv_opts.param_solver + -solver + #if " " in str($adv_opts.param_solver): + "$adv_opts.param_solver" + #else + $adv_opts.param_solver + #end if #end if #if $adv_opts.param_force: -force
--- a/readme.md Wed Mar 01 09:57:53 2017 -0500 +++ b/readme.md Tue Apr 18 15:48:45 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.: