Mercurial > repos > galaxyp > openms_mascotadapteronline
changeset 1:2e48052e1b95 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:42:24 -0400 |
| parents | 8746354dd6a9 |
| children | cd7e5dbbc988 |
| files | MascotAdapterOnline.xml readme.md |
| diffstat | 2 files changed, 26 insertions(+), 13 deletions(-) [+] |
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--- a/MascotAdapterOnline.xml Wed Mar 01 10:18:37 2017 -0500 +++ b/MascotAdapterOnline.xml Tue Apr 18 15:42:24 2017 -0400 @@ -34,13 +34,23 @@ -Mascot_parameters:precursor_mass_tolerance $param_Mascot_parameters_precursor_mass_tolerance #end if #if $param_Mascot_parameters_precursor_error_units: - -Mascot_parameters:precursor_error_units $param_Mascot_parameters_precursor_error_units + -Mascot_parameters:precursor_error_units + #if " " in str($param_Mascot_parameters_precursor_error_units): + "$param_Mascot_parameters_precursor_error_units" + #else + $param_Mascot_parameters_precursor_error_units + #end if #end if #if $param_Mascot_parameters_fragment_mass_tolerance: -Mascot_parameters:fragment_mass_tolerance $param_Mascot_parameters_fragment_mass_tolerance #end if #if $param_Mascot_parameters_fragment_error_units: - -Mascot_parameters:fragment_error_units $param_Mascot_parameters_fragment_error_units + -Mascot_parameters:fragment_error_units + #if " " in str($param_Mascot_parameters_fragment_error_units): + "$param_Mascot_parameters_fragment_error_units" + #else + $param_Mascot_parameters_fragment_error_units + #end if #end if #if $param_Mascot_parameters_charges: -Mascot_parameters:charges "$param_Mascot_parameters_charges" @@ -71,7 +81,12 @@ #end for #end if #if $param_Mascot_parameters_mass_type: - -Mascot_parameters:mass_type $param_Mascot_parameters_mass_type + -Mascot_parameters:mass_type + #if " " in str($param_Mascot_parameters_mass_type): + "$param_Mascot_parameters_mass_type" + #else + $param_Mascot_parameters_mass_type + #end if #end if #if $param_Mascot_parameters_number_of_hits: -Mascot_parameters:number_of_hits $param_Mascot_parameters_number_of_hits @@ -114,7 +129,12 @@ -force #end if #if $adv_opts.param_Mascot_parameters_search_type: - -Mascot_parameters:search_type $adv_opts.param_Mascot_parameters_search_type + -Mascot_parameters:search_type + #if " " in str($adv_opts.param_Mascot_parameters_search_type): + "$adv_opts.param_Mascot_parameters_search_type" + #else + $adv_opts.param_Mascot_parameters_search_type + #end if #end if #if $adv_opts.param_Mascot_parameters_special_modifications: -Mascot_parameters:special_modifications "$adv_opts.param_Mascot_parameters_special_modifications"
--- a/readme.md Wed Mar 01 10:18:37 2017 -0500 +++ b/readme.md Tue Apr 18 15:42:24 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.: