Mercurial > repos > galaxyp > openms_featurefinderidentification
changeset 1:6a3bbd5b8cb6 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 16:04:04 -0400 |
| parents | 3a61c78033f0 |
| children | d12500c4d67e |
| files | FeatureFinderIdentification.xml readme.md |
| diffstat | 2 files changed, 14 insertions(+), 11 deletions(-) [+] |
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--- a/FeatureFinderIdentification.xml Wed Mar 01 12:55:55 2017 -0500 +++ b/FeatureFinderIdentification.xml Tue Apr 18 16:04:04 2017 -0400 @@ -31,7 +31,12 @@ -trafo_out $param_trafo_out #end if #if $param_extract_reference_rt: - -extract:reference_rt $param_extract_reference_rt + -extract:reference_rt + #if " " in str($param_extract_reference_rt): + "$param_extract_reference_rt" + #else + $param_extract_reference_rt + #end if #end if #if $param_extract_rt_window: -extract:rt_window $param_extract_rt_window @@ -46,7 +51,12 @@ -detect:peak_width $param_detect_peak_width #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 $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force:
--- a/readme.md Wed Mar 01 12:55:55 2017 -0500 +++ b/readme.md Tue Apr 18 16:04:04 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.: