Mercurial > repos > galaxyp > openms_maprttransformer
changeset 1:bcb3f7dc36e1 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:41:44 -0400 |
| parents | 34e4f136ff49 |
| children | adb1e78506ff |
| files | MapRTTransformer.xml readme.md |
| diffstat | 2 files changed, 38 insertions(+), 15 deletions(-) [+] |
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--- a/MapRTTransformer.xml Wed Mar 01 10:00:22 2017 -0500 +++ b/MapRTTransformer.xml Tue Apr 18 15:41:44 2017 -0400 @@ -31,7 +31,12 @@ -store_original_rt #end if #if $param_model_type: - -model:type $param_model_type + -model:type + #if " " in str($param_model_type): + "$param_model_type" + #else + $param_model_type + #end if #end if #if $param_model_linear_symmetric_regression: -model:linear:symmetric_regression @@ -43,7 +48,12 @@ -model:b_spline:num_nodes $param_model_b_spline_num_nodes #end if #if $param_model_b_spline_extrapolate: - -model:b_spline:extrapolate $param_model_b_spline_extrapolate + -model:b_spline:extrapolate + #if " " in str($param_model_b_spline_extrapolate): + "$param_model_b_spline_extrapolate" + #else + $param_model_b_spline_extrapolate + #end if #end if #if $param_model_b_spline_boundary_condition: -model:b_spline:boundary_condition $param_model_b_spline_boundary_condition @@ -58,16 +68,36 @@ -model:lowess:delta $param_model_lowess_delta #end if #if $param_model_lowess_interpolation_type: - -model:lowess:interpolation_type $param_model_lowess_interpolation_type + -model:lowess:interpolation_type + #if " " in str($param_model_lowess_interpolation_type): + "$param_model_lowess_interpolation_type" + #else + $param_model_lowess_interpolation_type + #end if #end if #if $param_model_lowess_extrapolation_type: - -model:lowess:extrapolation_type $param_model_lowess_extrapolation_type + -model:lowess:extrapolation_type + #if " " in str($param_model_lowess_extrapolation_type): + "$param_model_lowess_extrapolation_type" + #else + $param_model_lowess_extrapolation_type + #end if #end if #if $param_model_interpolated_interpolation_type: - -model:interpolated:interpolation_type $param_model_interpolated_interpolation_type + -model:interpolated:interpolation_type + #if " " in str($param_model_interpolated_interpolation_type): + "$param_model_interpolated_interpolation_type" + #else + $param_model_interpolated_interpolation_type + #end if #end if #if $param_model_interpolated_extrapolation_type: - -model:interpolated:extrapolation_type $param_model_interpolated_extrapolation_type + -model:interpolated:extrapolation_type + #if " " in str($param_model_interpolated_extrapolation_type): + "$param_model_interpolated_extrapolation_type" + #else + $param_model_interpolated_extrapolation_type + #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force:
--- a/readme.md Wed Mar 01 10:00:22 2017 -0500 +++ b/readme.md Tue Apr 18 15:41:44 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.: