Mercurial > repos > galaxyp > openms_featurefindermultiplex
changeset 1:23d1e0b5cf9f draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 16:04:57 -0400 |
| parents | 14e0f052de8e |
| children | ca88bd28f116 |
| files | FeatureFinderMultiplex.xml readme.md |
| diffstat | 2 files changed, 14 insertions(+), 11 deletions(-) [+] |
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--- a/FeatureFinderMultiplex.xml Wed Mar 01 12:37:44 2017 -0500 +++ b/FeatureFinderMultiplex.xml Tue Apr 18 16:04:57 2017 -0400 @@ -40,7 +40,12 @@ -algorithm:mz_tolerance $param_algorithm_mz_tolerance #end if #if $param_algorithm_mz_unit: - -algorithm:mz_unit $param_algorithm_mz_unit + -algorithm:mz_unit + #if " " in str($param_algorithm_mz_unit): + "$param_algorithm_mz_unit" + #else + $param_algorithm_mz_unit + #end if #end if #if $param_algorithm_intensity_cutoff: -algorithm:intensity_cutoff $param_algorithm_intensity_cutoff @@ -68,7 +73,12 @@ -algorithm:knock_out #end if #if $adv_opts.param_algorithm_averagine_type: - -algorithm:averagine_type $adv_opts.param_algorithm_averagine_type + -algorithm:averagine_type + #if " " in str($adv_opts.param_algorithm_averagine_type): + "$adv_opts.param_algorithm_averagine_type" + #else + $adv_opts.param_algorithm_averagine_type + #end if #end if #if $adv_opts.param_labels_Arg6: -labels:Arg6 $adv_opts.param_labels_Arg6
--- a/readme.md Wed Mar 01 12:37:44 2017 -0500 +++ b/readme.md Tue Apr 18 16:04:57 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.: