Mercurial > repos > galaxyp > openms_metaprosip
changeset 1:5fc08238d0ce draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author | galaxyp |
---|---|
date | Tue, 18 Apr 2017 15:43:02 -0400 |
parents | 0283517872f8 |
children | 233c29ce2753 |
files | MetaProSIP.xml readme.md |
diffstat | 2 files changed, 20 insertions(+), 12 deletions(-) [+] |
line wrap: on
line diff
--- a/MetaProSIP.xml Wed Mar 01 10:09:33 2017 -0500 +++ b/MetaProSIP.xml Tue Apr 18 15:43:02 2017 -0400 @@ -52,13 +52,23 @@ -weight_merge_window $param_weight_merge_window #end if #if $param_plot_extension: - -plot_extension $param_plot_extension + -plot_extension + #if " " in str($param_plot_extension): + "$param_plot_extension" + #else + $param_plot_extension + #end if #end if #if $param_qc_output_directory: -qc_output_directory "$param_qc_output_directory" #end if #if $param_labeling_element: - -labeling_element $param_labeling_element + -labeling_element + #if " " in str($param_labeling_element): + "$param_labeling_element" + #else + $param_labeling_element + #end if #end if #if $param_use_unassigned_ids: -use_unassigned_ids @@ -104,7 +114,12 @@ -score_plot_yaxis_min $adv_opts.param_score_plot_yaxis_min #end if #if $adv_opts.param_collect_method: - -collect_method $adv_opts.param_collect_method + -collect_method + #if " " in str($adv_opts.param_collect_method): + "$adv_opts.param_collect_method" + #else + $adv_opts.param_collect_method + #end if #end if #if $adv_opts.param_lowRIA_correlation_threshold: -lowRIA_correlation_threshold $adv_opts.param_lowRIA_correlation_threshold
--- a/readme.md Wed Mar 01 10:09:33 2017 -0500 +++ b/readme.md Tue Apr 18 15:43:02 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.: