Mercurial > repos > galaxyp > openms_mrmtransitiongrouppicker
changeset 1:96c52704abcd draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:40:38 -0400 |
| parents | 006142eda968 |
| children | 42ff199c97a8 |
| files | MRMTransitionGroupPicker.xml readme.md |
| diffstat | 2 files changed, 26 insertions(+), 13 deletions(-) [+] |
line wrap: on
line diff
--- a/MRMTransitionGroupPicker.xml Wed Mar 01 10:08:42 2017 -0500 +++ b/MRMTransitionGroupPicker.xml Tue Apr 18 15:40:38 2017 -0400 @@ -36,7 +36,12 @@ -algorithm:PeakPickerMRM:gauss_width $param_algorithm_PeakPickerMRM_gauss_width #end if #if $param_algorithm_PeakPickerMRM_use_gauss: - -algorithm:PeakPickerMRM:use_gauss $param_algorithm_PeakPickerMRM_use_gauss + -algorithm:PeakPickerMRM:use_gauss + #if " " in str($param_algorithm_PeakPickerMRM_use_gauss): + "$param_algorithm_PeakPickerMRM_use_gauss" + #else + $param_algorithm_PeakPickerMRM_use_gauss + #end if #end if #if $param_algorithm_PeakPickerMRM_peak_width: -algorithm:PeakPickerMRM:peak_width $param_algorithm_PeakPickerMRM_peak_width @@ -51,13 +56,23 @@ -algorithm:PeakPickerMRM:sn_bin_count $param_algorithm_PeakPickerMRM_sn_bin_count #end if #if $param_algorithm_PeakPickerMRM_write_sn_log_messages: - -algorithm:PeakPickerMRM:write_sn_log_messages $param_algorithm_PeakPickerMRM_write_sn_log_messages + -algorithm:PeakPickerMRM:write_sn_log_messages + #if " " in str($param_algorithm_PeakPickerMRM_write_sn_log_messages): + "$param_algorithm_PeakPickerMRM_write_sn_log_messages" + #else + $param_algorithm_PeakPickerMRM_write_sn_log_messages + #end if #end if #if $param_algorithm_PeakPickerMRM_remove_overlapping_peaks: -algorithm:PeakPickerMRM:remove_overlapping_peaks #end if #if $param_algorithm_PeakPickerMRM_method: - -algorithm:PeakPickerMRM:method $param_algorithm_PeakPickerMRM_method + -algorithm:PeakPickerMRM:method + #if " " in str($param_algorithm_PeakPickerMRM_method): + "$param_algorithm_PeakPickerMRM_method" + #else + $param_algorithm_PeakPickerMRM_method + #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: @@ -67,7 +82,12 @@ -algorithm:min_peak_width $adv_opts.param_algorithm_min_peak_width #end if #if $adv_opts.param_algorithm_background_subtraction: - -algorithm:background_subtraction $adv_opts.param_algorithm_background_subtraction + -algorithm:background_subtraction + #if " " in str($adv_opts.param_algorithm_background_subtraction): + "$adv_opts.param_algorithm_background_subtraction" + #else + $adv_opts.param_algorithm_background_subtraction + #end if #end if #if $adv_opts.param_algorithm_recalculate_peaks: -algorithm:recalculate_peaks "$adv_opts.param_algorithm_recalculate_peaks"
--- a/readme.md Wed Mar 01 10:08:42 2017 -0500 +++ b/readme.md Tue Apr 18 15:40:38 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.: