Mercurial > repos > galaxyp > openms_svmtheoreticalspectrumgeneratortrainer
changeset 1:773e6b46489a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:55:47 -0400 |
| parents | 2b1637506673 |
| children | a8a1079d4880 |
| files | SvmTheoreticalSpectrumGeneratorTrainer.xml readme.md |
| diffstat | 2 files changed, 26 insertions(+), 13 deletions(-) [+] |
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--- a/SvmTheoreticalSpectrumGeneratorTrainer.xml Wed Mar 01 10:06:57 2017 -0500 +++ b/SvmTheoreticalSpectrumGeneratorTrainer.xml Tue Apr 18 15:55:47 2017 -0400 @@ -40,10 +40,20 @@ -algorithm:peak_tolerance $param_algorithm_peak_tolerance #end if #if $param_algorithm_add_b_ions: - -algorithm:add_b_ions $param_algorithm_add_b_ions + -algorithm:add_b_ions + #if " " in str($param_algorithm_add_b_ions): + "$param_algorithm_add_b_ions" + #else + $param_algorithm_add_b_ions + #end if #end if #if $param_algorithm_add_y_ions: - -algorithm:add_y_ions $param_algorithm_add_y_ions + -algorithm:add_y_ions + #if " " in str($param_algorithm_add_y_ions): + "$param_algorithm_add_y_ions" + #else + $param_algorithm_add_y_ions + #end if #end if #if $param_algorithm_add_a_ions: -algorithm:add_a_ions @@ -73,7 +83,12 @@ -algorithm:svm:svr_type $param_algorithm_svm_svr_type #end if #if $param_algorithm_svm_scaling: - -algorithm:svm:scaling $param_algorithm_svm_scaling + -algorithm:svm:scaling + #if " " in str($param_algorithm_svm_scaling): + "$param_algorithm_svm_scaling" + #else + $param_algorithm_svm_scaling + #end if #end if #if $param_algorithm_svm_scaling_lower: -algorithm:svm:scaling_lower $param_algorithm_svm_scaling_lower @@ -106,7 +121,12 @@ -algorithm:svm:svc:nu $param_algorithm_svm_svc_nu #end if #if $param_algorithm_svm_svc_balancing: - -algorithm:svm:svc:balancing $param_algorithm_svm_svc_balancing + -algorithm:svm:svc:balancing + #if " " in str($param_algorithm_svm_svc_balancing): + "$param_algorithm_svm_svc_balancing" + #else + $param_algorithm_svm_svc_balancing + #end if #end if #if $param_algorithm_svm_svc_degree_start: -algorithm:svm:svc:degree_start $param_algorithm_svm_svc_degree_start
--- a/readme.md Wed Mar 01 10:06:57 2017 -0500 +++ b/readme.md Tue Apr 18 15:55:47 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.: