Mercurial > repos > galaxyp > openms_simplesearchengine
changeset 1:0ca8724c404a draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:52:58 -0400 (2017-04-18) |
| parents | 2f4218b98805 |
| children | 8e4cbb4c3c71 |
| files | SimpleSearchEngine.xml readme.md |
| diffstat | 2 files changed, 20 insertions(+), 12 deletions(-) [+] |
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--- a/SimpleSearchEngine.xml Wed Mar 01 10:10:25 2017 -0500 +++ b/SimpleSearchEngine.xml Tue Apr 18 15:52:58 2017 -0400 @@ -22,19 +22,34 @@ -out $param_out #end if #if $param_enzyme: - -enzyme $param_enzyme + -enzyme + #if " " in str($param_enzyme): + "$param_enzyme" + #else + $param_enzyme + #end if #end if #if $param_precursor_mass_tolerance: -precursor:mass_tolerance $param_precursor_mass_tolerance #end if #if $param_precursor_mass_tolerance_unit: - -precursor:mass_tolerance_unit $param_precursor_mass_tolerance_unit + -precursor:mass_tolerance_unit + #if " " in str($param_precursor_mass_tolerance_unit): + "$param_precursor_mass_tolerance_unit" + #else + $param_precursor_mass_tolerance_unit + #end if #end if #if $param_fragment_mass_tolerance: -fragment:mass_tolerance $param_fragment_mass_tolerance #end if #if $param_fragment_mass_tolerance_unit: - -fragment:mass_tolerance_unit $param_fragment_mass_tolerance_unit + -fragment:mass_tolerance_unit + #if " " in str($param_fragment_mass_tolerance_unit): + "$param_fragment_mass_tolerance_unit" + #else + $param_fragment_mass_tolerance_unit + #end if #end if #if $rep_param_modifications_fixed:
--- a/readme.md Wed Mar 01 10:10:25 2017 -0500 +++ b/readme.md Tue Apr 18 15:52:58 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.: