Mercurial > repos > galaxyp > openms_featurefindermetabo
changeset 1:15cc4acac8c3 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 16:04:46 -0400 |
| parents | 2602a6da5ad3 |
| children | 3256eccfdaa7 |
| files | FeatureFinderMetabo.xml readme.md |
| diffstat | 2 files changed, 50 insertions(+), 17 deletions(-) [+] |
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--- a/FeatureFinderMetabo.xml Wed Mar 01 12:21:06 2017 -0500 +++ b/FeatureFinderMetabo.xml Tue Apr 18 16:04:46 2017 -0400 @@ -31,16 +31,36 @@ -algorithm:mtd:mass_error_ppm $param_algorithm_mtd_mass_error_ppm #end if #if $param_algorithm_mtd_reestimate_mt_sd: - -algorithm:mtd:reestimate_mt_sd $param_algorithm_mtd_reestimate_mt_sd + -algorithm:mtd:reestimate_mt_sd + #if " " in str($param_algorithm_mtd_reestimate_mt_sd): + "$param_algorithm_mtd_reestimate_mt_sd" + #else + $param_algorithm_mtd_reestimate_mt_sd + #end if #end if #if $param_algorithm_mtd_quant_method: - -algorithm:mtd:quant_method $param_algorithm_mtd_quant_method + -algorithm:mtd:quant_method + #if " " in str($param_algorithm_mtd_quant_method): + "$param_algorithm_mtd_quant_method" + #else + $param_algorithm_mtd_quant_method + #end if #end if #if $param_algorithm_epd_enabled: - -algorithm:epd:enabled $param_algorithm_epd_enabled + -algorithm:epd:enabled + #if " " in str($param_algorithm_epd_enabled): + "$param_algorithm_epd_enabled" + #else + $param_algorithm_epd_enabled + #end if #end if #if $param_algorithm_epd_width_filtering: - -algorithm:epd:width_filtering $param_algorithm_epd_width_filtering + -algorithm:epd:width_filtering + #if " " in str($param_algorithm_epd_width_filtering): + "$param_algorithm_epd_width_filtering" + #else + $param_algorithm_epd_width_filtering + #end if #end if #if $param_algorithm_ffm_charge_lower_bound: -algorithm:ffm:charge_lower_bound $param_algorithm_ffm_charge_lower_bound @@ -49,10 +69,20 @@ -algorithm:ffm:charge_upper_bound $param_algorithm_ffm_charge_upper_bound #end if #if $param_algorithm_ffm_enable_RT_filtering: - -algorithm:ffm:enable_RT_filtering $param_algorithm_ffm_enable_RT_filtering + -algorithm:ffm:enable_RT_filtering + #if " " in str($param_algorithm_ffm_enable_RT_filtering): + "$param_algorithm_ffm_enable_RT_filtering" + #else + $param_algorithm_ffm_enable_RT_filtering + #end if #end if #if $param_algorithm_ffm_isotope_filtering_model: - -algorithm:ffm:isotope_filtering_model $param_algorithm_ffm_isotope_filtering_model + -algorithm:ffm:isotope_filtering_model + #if " " in str($param_algorithm_ffm_isotope_filtering_model): + "$param_algorithm_ffm_isotope_filtering_model" + #else + $param_algorithm_ffm_isotope_filtering_model + #end if #end if #if $param_algorithm_ffm_mz_scoring_13C: -algorithm:ffm:mz_scoring_13C @@ -65,7 +95,12 @@ -force #end if #if $adv_opts.param_algorithm_mtd_trace_termination_criterion: - -algorithm:mtd:trace_termination_criterion $adv_opts.param_algorithm_mtd_trace_termination_criterion + -algorithm:mtd:trace_termination_criterion + #if " " in str($adv_opts.param_algorithm_mtd_trace_termination_criterion): + "$adv_opts.param_algorithm_mtd_trace_termination_criterion" + #else + $adv_opts.param_algorithm_mtd_trace_termination_criterion + #end if #end if #if $adv_opts.param_algorithm_mtd_trace_termination_outliers: -algorithm:mtd:trace_termination_outliers $adv_opts.param_algorithm_mtd_trace_termination_outliers @@ -98,7 +133,12 @@ -algorithm:ffm:report_summed_ints #end if #if $adv_opts.param_algorithm_ffm_use_smoothed_intensities: - -algorithm:ffm:use_smoothed_intensities $adv_opts.param_algorithm_ffm_use_smoothed_intensities + -algorithm:ffm:use_smoothed_intensities + #if " " in str($adv_opts.param_algorithm_ffm_use_smoothed_intensities): + "$adv_opts.param_algorithm_ffm_use_smoothed_intensities" + #else + $adv_opts.param_algorithm_ffm_use_smoothed_intensities + #end if #end if #end if </command>
--- a/readme.md Wed Mar 01 12:21:06 2017 -0500 +++ b/readme.md Tue Apr 18 16:04:46 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.: