Mercurial > repos > galaxyp > openms_spectramerger
changeset 1:4726f1062f33 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:55:34 -0400 |
| parents | c561e6fb46d8 |
| children | 77270633cbc8 |
| files | SpectraMerger.xml readme.md |
| diffstat | 2 files changed, 38 insertions(+), 15 deletions(-) [+] |
line wrap: on
line diff
--- a/SpectraMerger.xml Wed Mar 01 10:11:40 2017 -0500 +++ b/SpectraMerger.xml Tue Apr 18 15:55:34 2017 -0400 @@ -19,10 +19,20 @@ -out $param_out #end if #if $param_merging_method: - -merging_method $param_merging_method + -merging_method + #if " " in str($param_merging_method): + "$param_merging_method" + #else + $param_merging_method + #end if #end if #if $param_algorithm_average_gaussian_spectrum_type: - -algorithm:average_gaussian:spectrum_type $param_algorithm_average_gaussian_spectrum_type + -algorithm:average_gaussian:spectrum_type + #if " " in str($param_algorithm_average_gaussian_spectrum_type): + "$param_algorithm_average_gaussian_spectrum_type" + #else + $param_algorithm_average_gaussian_spectrum_type + #end if #end if #if $param_algorithm_average_gaussian_ms_level: -algorithm:average_gaussian:ms_level $param_algorithm_average_gaussian_ms_level @@ -31,7 +41,12 @@ -algorithm:average_gaussian:rt_FWHM $param_algorithm_average_gaussian_rt_FWHM #end if #if $param_algorithm_average_tophat_spectrum_type: - -algorithm:average_tophat:spectrum_type $param_algorithm_average_tophat_spectrum_type + -algorithm:average_tophat:spectrum_type + #if " " in str($param_algorithm_average_tophat_spectrum_type): + "$param_algorithm_average_tophat_spectrum_type" + #else + $param_algorithm_average_tophat_spectrum_type + #end if #end if #if $param_algorithm_average_tophat_ms_level: -algorithm:average_tophat:ms_level $param_algorithm_average_tophat_ms_level @@ -40,7 +55,12 @@ -algorithm:average_tophat:rt_range $param_algorithm_average_tophat_rt_range #end if #if $param_algorithm_average_tophat_rt_unit: - -algorithm:average_tophat:rt_unit $param_algorithm_average_tophat_rt_unit + -algorithm:average_tophat:rt_unit + #if " " in str($param_algorithm_average_tophat_rt_unit): + "$param_algorithm_average_tophat_rt_unit" + #else + $param_algorithm_average_tophat_rt_unit + #end if #end if #if $rep_param_algorithm_block_method_ms_levels: @@ -73,10 +93,20 @@ -algorithm:mz_binning_width $adv_opts.param_algorithm_mz_binning_width #end if #if $adv_opts.param_algorithm_mz_binning_width_unit: - -algorithm:mz_binning_width_unit $adv_opts.param_algorithm_mz_binning_width_unit + -algorithm:mz_binning_width_unit + #if " " in str($adv_opts.param_algorithm_mz_binning_width_unit): + "$adv_opts.param_algorithm_mz_binning_width_unit" + #else + $adv_opts.param_algorithm_mz_binning_width_unit + #end if #end if #if $adv_opts.param_algorithm_sort_blocks: - -algorithm:sort_blocks $adv_opts.param_algorithm_sort_blocks + -algorithm:sort_blocks + #if " " in str($adv_opts.param_algorithm_sort_blocks): + "$adv_opts.param_algorithm_sort_blocks" + #else + $adv_opts.param_algorithm_sort_blocks + #end if #end if #if $adv_opts.param_algorithm_average_gaussian_cutoff: -algorithm:average_gaussian:cutoff $adv_opts.param_algorithm_average_gaussian_cutoff
--- a/readme.md Wed Mar 01 10:11:40 2017 -0500 +++ b/readme.md Tue Apr 18 15:55:34 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.: