Mercurial > repos > galaxyp > openms_peakpickerhires
changeset 1:8d74240aafb9 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
author | galaxyp |
---|---|
date | Tue, 18 Apr 2017 15:47:38 -0400 |
parents | 2741adc39601 |
children | a70b8ea9765a |
files | PeakPickerHiRes.xml readme.md |
diffstat | 2 files changed, 20 insertions(+), 12 deletions(-) [+] |
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--- a/PeakPickerHiRes.xml Wed Mar 01 09:58:38 2017 -0500 +++ b/PeakPickerHiRes.xml Tue Apr 18 15:47:38 2017 -0400 @@ -36,7 +36,12 @@ -algorithm:report_FWHM #end if #if $param_algorithm_report_FWHM_unit: - -algorithm:report_FWHM_unit "$param_algorithm_report_FWHM_unit" + -algorithm:report_FWHM_unit + #if " " in str($param_algorithm_report_FWHM_unit): + "$param_algorithm_report_FWHM_unit" + #else + $param_algorithm_report_FWHM_unit + #end if #end if #if $param_algorithm_SignalToNoise_win_len: -algorithm:SignalToNoise:win_len $param_algorithm_SignalToNoise_win_len @@ -48,11 +53,21 @@ -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements #end if #if $param_algorithm_SignalToNoise_write_log_messages: - -algorithm:SignalToNoise:write_log_messages $param_algorithm_SignalToNoise_write_log_messages + -algorithm:SignalToNoise:write_log_messages + #if " " in str($param_algorithm_SignalToNoise_write_log_messages): + "$param_algorithm_SignalToNoise_write_log_messages" + #else + $param_algorithm_SignalToNoise_write_log_messages + #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_processOption: - -processOption $adv_opts.param_processOption + -processOption + #if " " in str($adv_opts.param_processOption): + "$adv_opts.param_processOption" + #else + $adv_opts.param_processOption + #end if #end if #if $adv_opts.param_force: -force
--- a/readme.md Wed Mar 01 09:58:38 2017 -0500 +++ b/readme.md Tue Apr 18 15:47:38 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.: