Mercurial > repos > galaxyp > openms_featurefindercentroided
changeset 1:9e6a24fc4f4a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 16:03:41 -0400 |
| parents | 7dd3b4327a17 |
| children | b8cce52343c2 |
| files | FeatureFinderCentroided.xml readme.md |
| diffstat | 2 files changed, 14 insertions(+), 11 deletions(-) [+] |
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--- a/FeatureFinderCentroided.xml Wed Mar 01 12:29:02 2017 -0500 +++ b/FeatureFinderCentroided.xml Tue Apr 18 16:03:41 2017 -0400 @@ -55,7 +55,12 @@ -algorithm:feature:min_score $param_algorithm_feature_min_score #end if #if $param_algorithm_feature_reported_mz: - -algorithm:feature:reported_mz $param_algorithm_feature_reported_mz + -algorithm:feature:reported_mz + #if " " in str($param_algorithm_feature_reported_mz): + "$param_algorithm_feature_reported_mz" + #else + $param_algorithm_feature_reported_mz + #end if #end if #if $param_algorithm_user_seed_rt_tolerance: -algorithm:user-seed:rt_tolerance $param_algorithm_user_seed_rt_tolerance @@ -107,7 +112,12 @@ -algorithm:feature:max_rt_span $adv_opts.param_algorithm_feature_max_rt_span #end if #if $adv_opts.param_algorithm_feature_rt_shape: - -algorithm:feature:rt_shape $adv_opts.param_algorithm_feature_rt_shape + -algorithm:feature:rt_shape + #if " " in str($adv_opts.param_algorithm_feature_rt_shape): + "$adv_opts.param_algorithm_feature_rt_shape" + #else + $adv_opts.param_algorithm_feature_rt_shape + #end if #end if #if $adv_opts.param_algorithm_feature_max_intersection: -algorithm:feature:max_intersection $adv_opts.param_algorithm_feature_max_intersection
--- a/readme.md Wed Mar 01 12:29:02 2017 -0500 +++ b/readme.md Tue Apr 18 16:03:41 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.: