Mercurial > repos > galaxyp > openms_consensusid
changeset 1:66388c2e2f38 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:59:22 -0400 |
| parents | 5c56387ff06a |
| children | 8960fb791701 |
| files | ConsensusID.xml readme.md |
| diffstat | 2 files changed, 14 insertions(+), 11 deletions(-) [+] |
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--- a/ConsensusID.xml Wed Mar 01 12:40:02 2017 -0500 +++ b/ConsensusID.xml Tue Apr 18 15:59:22 2017 -0400 @@ -25,7 +25,12 @@ -mz_delta $param_mz_delta #end if #if $param_algorithm: - -algorithm $param_algorithm + -algorithm + #if " " in str($param_algorithm): + "$param_algorithm" + #else + $param_algorithm + #end if #end if #if $param_filter_considered_hits: -filter:considered_hits $param_filter_considered_hits @@ -43,7 +48,12 @@ -PEPIons:min_shared $param_PEPIons_min_shared #end if #if $param_PEPMatrix_matrix: - -PEPMatrix:matrix $param_PEPMatrix_matrix + -PEPMatrix:matrix + #if " " in str($param_PEPMatrix_matrix): + "$param_PEPMatrix_matrix" + #else + $param_PEPMatrix_matrix + #end if #end if #if $param_PEPMatrix_penalty: -PEPMatrix:penalty $param_PEPMatrix_penalty
--- a/readme.md Wed Mar 01 12:40:02 2017 -0500 +++ b/readme.md Tue Apr 18 15:59:22 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.: