Mercurial > repos > galaxyp > openms_decoydatabase
changeset 1:112ff589ce35 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:29:47 -0400 |
| parents | bb36816527e8 |
| children | e1e2adf6209f |
| files | DecoyDatabase.xml readme.md |
| diffstat | 2 files changed, 26 insertions(+), 20 deletions(-) [+] |
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--- a/DecoyDatabase.xml Wed Mar 01 09:55:50 2017 -0500 +++ b/DecoyDatabase.xml Tue Apr 18 15:29:47 2017 -0400 @@ -23,13 +23,28 @@ -decoy_string "$param_decoy_string" #end if #if $param_decoy_string_position: - -decoy_string_position $param_decoy_string_position + -decoy_string_position + #if " " in str($param_decoy_string_position): + "$param_decoy_string_position" + #else + $param_decoy_string_position + #end if #end if #if $param_append: - -append $param_append + -append + #if " " in str($param_append): + "$param_append" + #else + $param_append + #end if #end if #if $param_method: - -method $param_method + -method + #if " " in str($param_method): + "$param_method" + #else + $param_method + #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force: @@ -73,14 +88,12 @@ <outputs> <data name="param_out" format="fasta"/> </outputs> - - <tests> - <test> - <param name="param_in" value="DecoyDatabase_input.fasta"/> - <output name="param_out" file="DecoyDatabase_output.fasta"/> - </test> - </tests> - + <tests> + <test> + <param name="param_in" value="DecoyDatabase_input.fasta"/> + <output name="param_out" file="DecoyDatabase_output.fasta"/> + </test> + </tests> <help>Create decoy peptide databases from normal ones.
--- a/readme.md Wed Mar 01 09:55:50 2017 -0500 +++ b/readme.md Tue Apr 18 15:29:47 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.: