Mercurial > repos > galaxyp > openms_inclusionexclusionlistcreator
changeset 1:b72178f15198 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:38:26 -0400 |
| parents | 3ef378e41673 |
| children | 264907e4d32a |
| files | InclusionExclusionListCreator.xml readme.md |
| diffstat | 2 files changed, 26 insertions(+), 13 deletions(-) [+] |
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--- a/InclusionExclusionListCreator.xml Wed Mar 01 10:02:07 2017 -0500 +++ b/InclusionExclusionListCreator.xml Tue Apr 18 15:38:26 2017 -0400 @@ -39,7 +39,12 @@ #end for #end if #if $param_inclusion_strategy: - -inclusion_strategy $param_inclusion_strategy + -inclusion_strategy + #if " " in str($param_inclusion_strategy): + "$param_inclusion_strategy" + #else + $param_inclusion_strategy + #end if #end if #if $rep_param_exclusion_charges: @@ -59,10 +64,20 @@ -algorithm:InclusionExclusionList:missed_cleavages $param_algorithm_InclusionExclusionList_missed_cleavages #end if #if $param_algorithm_InclusionExclusionList_RT_unit: - -algorithm:InclusionExclusionList:RT:unit $param_algorithm_InclusionExclusionList_RT_unit + -algorithm:InclusionExclusionList:RT:unit + #if " " in str($param_algorithm_InclusionExclusionList_RT_unit): + "$param_algorithm_InclusionExclusionList_RT_unit" + #else + $param_algorithm_InclusionExclusionList_RT_unit + #end if #end if #if $param_algorithm_InclusionExclusionList_RT_use_relative: - -algorithm:InclusionExclusionList:RT:use_relative $param_algorithm_InclusionExclusionList_RT_use_relative + -algorithm:InclusionExclusionList:RT:use_relative + #if " " in str($param_algorithm_InclusionExclusionList_RT_use_relative): + "$param_algorithm_InclusionExclusionList_RT_use_relative" + #else + $param_algorithm_InclusionExclusionList_RT_use_relative + #end if #end if #if $param_algorithm_InclusionExclusionList_RT_window_relative: -algorithm:InclusionExclusionList:RT:window_relative $param_algorithm_InclusionExclusionList_RT_window_relative @@ -74,7 +89,12 @@ -algorithm:InclusionExclusionList:merge:mz_tol $param_algorithm_InclusionExclusionList_merge_mz_tol #end if #if $param_algorithm_InclusionExclusionList_merge_mz_tol_unit: - -algorithm:InclusionExclusionList:merge:mz_tol_unit $param_algorithm_InclusionExclusionList_merge_mz_tol_unit + -algorithm:InclusionExclusionList:merge:mz_tol_unit + #if " " in str($param_algorithm_InclusionExclusionList_merge_mz_tol_unit): + "$param_algorithm_InclusionExclusionList_merge_mz_tol_unit" + #else + $param_algorithm_InclusionExclusionList_merge_mz_tol_unit + #end if #end if #if $param_algorithm_InclusionExclusionList_merge_rt_tol: -algorithm:InclusionExclusionList:merge:rt_tol $param_algorithm_InclusionExclusionList_merge_rt_tol
--- a/readme.md Wed Mar 01 10:02:07 2017 -0500 +++ b/readme.md Tue Apr 18 15:38:26 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.: