Mercurial > repos > galaxyp > openms_filefilter
changeset 1:2c3736b75339 draft
planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/openms commit 820d990f9217706e693b8a2f1da91e13c09cb0fb
| author | galaxyp |
|---|---|
| date | Tue, 18 Apr 2017 15:34:13 -0400 |
| parents | c0bf230a772c |
| children | 983e089f5cc5 |
| files | FileFilter.xml readme.md |
| diffstat | 2 files changed, 38 insertions(+), 15 deletions(-) [+] |
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--- a/FileFilter.xml Wed Mar 01 10:17:49 2017 -0500 +++ b/FileFilter.xml Tue Apr 18 15:34:13 2017 -0400 @@ -87,22 +87,42 @@ -peak_options:remove_chromatograms #end if #if $param_peak_options_mz_precision: - -peak_options:mz_precision $param_peak_options_mz_precision + -peak_options:mz_precision + #if " " in str($param_peak_options_mz_precision): + "$param_peak_options_mz_precision" + #else + $param_peak_options_mz_precision + #end if #end if #if $param_peak_options_int_precision: - -peak_options:int_precision $param_peak_options_int_precision + -peak_options:int_precision + #if " " in str($param_peak_options_int_precision): + "$param_peak_options_int_precision" + #else + $param_peak_options_int_precision + #end if #end if #if $param_peak_options_indexed_file: -peak_options:indexed_file #end if #if $param_peak_options_numpress_masstime: - -peak_options:numpress:masstime $param_peak_options_numpress_masstime + -peak_options:numpress:masstime + #if " " in str($param_peak_options_numpress_masstime): + "$param_peak_options_numpress_masstime" + #else + $param_peak_options_numpress_masstime + #end if #end if #if $param_peak_options_numpress_masstime_error: -peak_options:numpress:masstime_error $param_peak_options_numpress_masstime_error #end if #if $param_peak_options_numpress_intensity: - -peak_options:numpress:intensity $param_peak_options_numpress_intensity + -peak_options:numpress:intensity + #if " " in str($param_peak_options_numpress_intensity): + "$param_peak_options_numpress_intensity" + #else + $param_peak_options_numpress_intensity + #end if #end if #if $param_peak_options_numpress_intensity_error: -peak_options:numpress:intensity_error $param_peak_options_numpress_intensity_error @@ -183,7 +203,12 @@ -consensus:map_and #end if #if $param_consensus_blackorwhitelist_blacklist: - -consensus:blackorwhitelist:blacklist $param_consensus_blackorwhitelist_blacklist + -consensus:blackorwhitelist:blacklist + #if " " in str($param_consensus_blackorwhitelist_blacklist): + "$param_consensus_blackorwhitelist_blacklist" + #else + $param_consensus_blackorwhitelist_blacklist + #end if #end if #if $param_consensus_blackorwhitelist_file: -consensus:blackorwhitelist:file $param_consensus_blackorwhitelist_file @@ -281,7 +306,12 @@ -algorithm:SignalToNoise:min_required_elements $param_algorithm_SignalToNoise_min_required_elements #end if #if $param_algorithm_SignalToNoise_write_log_messages: - -algorithm:SignalToNoise:write_log_messages $param_algorithm_SignalToNoise_write_log_messages + -algorithm:SignalToNoise:write_log_messages + #if " " in str($param_algorithm_SignalToNoise_write_log_messages): + "$param_algorithm_SignalToNoise_write_log_messages" + #else + $param_algorithm_SignalToNoise_write_log_messages + #end if #end if #if $adv_opts.adv_opts_selector=='advanced': #if $adv_opts.param_force:
--- a/readme.md Wed Mar 01 10:17:49 2017 -0500 +++ b/readme.md Tue Apr 18 15:34:13 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.: