Mercurial > repos > galaxyp > openms_isobaricanalyzer
changeset 2:ef60d1479807 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:39:06 -0400 |
| parents | fd36e0bbb6a2 |
| children | eb2f29cfe471 |
| files | IsobaricAnalyzer.xml readme.md |
| diffstat | 2 files changed, 38 insertions(+), 15 deletions(-) [+] |
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--- a/IsobaricAnalyzer.xml Sat Apr 08 08:30:24 2017 -0400 +++ b/IsobaricAnalyzer.xml Tue Apr 18 15:39:06 2017 -0400 @@ -13,7 +13,12 @@ <command>IsobaricAnalyzer #if $param_type: - -type $param_type + -type + #if " " in str($param_type): + "$param_type" + #else + $param_type + #end if #end if #if $param_in: -in $param_in @@ -25,7 +30,12 @@ -id_pool "$param_id_pool" #end if #if $param_extraction_select_activation: - -extraction:select_activation '$param_extraction_select_activation' + -extraction:select_activation + #if " " in str($param_extraction_select_activation): + "$param_extraction_select_activation" + #else + $param_extraction_select_activation + #end if #end if #if $param_extraction_reporter_mass_shift: -extraction:reporter_mass_shift $param_extraction_reporter_mass_shift @@ -34,7 +44,12 @@ -extraction:min_precursor_intensity $param_extraction_min_precursor_intensity #end if #if $param_extraction_keep_unannotated_precursor: - -extraction:keep_unannotated_precursor $param_extraction_keep_unannotated_precursor + -extraction:keep_unannotated_precursor + #if " " in str($param_extraction_keep_unannotated_precursor): + "$param_extraction_keep_unannotated_precursor" + #else + $param_extraction_keep_unannotated_precursor + #end if #end if #if $param_extraction_min_reporter_intensity: -extraction:min_reporter_intensity $param_extraction_min_reporter_intensity @@ -110,7 +125,12 @@ #end for #end if #if $param_quantification_isotope_correction: - -quantification:isotope_correction $param_quantification_isotope_correction + -quantification:isotope_correction + #if " " in str($param_quantification_isotope_correction): + "$param_quantification_isotope_correction" + #else + $param_quantification_isotope_correction + #end if #end if #if $param_quantification_normalization: -quantification:normalization @@ -146,7 +166,12 @@ -tmt10plex:channel_131_description "$param_tmt10plex_channel_131_description" #end if #if $param_tmt10plex_reference_channel: - -tmt10plex:reference_channel $param_tmt10plex_reference_channel + -tmt10plex:reference_channel + #if " " in str($param_tmt10plex_reference_channel): + "$param_tmt10plex_reference_channel" + #else + $param_tmt10plex_reference_channel + #end if #end if #if $rep_param_tmt10plex_correction_matrix: @@ -199,7 +224,12 @@ -extraction:precursor_isotope_deviation $adv_opts.param_extraction_precursor_isotope_deviation #end if #if $adv_opts.param_extraction_purity_interpolation: - -extraction:purity_interpolation $adv_opts.param_extraction_purity_interpolation + -extraction:purity_interpolation + #if " " in str($adv_opts.param_extraction_purity_interpolation): + "$adv_opts.param_extraction_purity_interpolation" + #else + $adv_opts.param_extraction_purity_interpolation + #end if #end if #end if </command>
--- a/readme.md Sat Apr 08 08:30:24 2017 -0400 +++ b/readme.md Tue Apr 18 15:39:06 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.: