Mercurial > repos > sanbi-uwc > confil
changeset 2:ca3c6f955c3e draft
planemo upload for repository https://github.com/COMBAT-TB/confil commit 692db20f6abdd864953054c4c8c43d5192a87e3d
author | sanbi-uwc |
---|---|
date | Thu, 14 Feb 2019 04:36:14 -0500 |
parents | d5b37a19547a |
children | 53a61865e86e |
files | confil.xml |
diffstat | 1 files changed, 20 insertions(+), 7 deletions(-) [+] |
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--- a/confil.xml Wed Feb 13 09:02:41 2019 -0500 +++ b/confil.xml Thu Feb 14 04:36:14 2019 -0500 @@ -3,16 +3,29 @@ <requirement type="package" version="7.0">click</requirement> </requirements> <command detect_errors="exit_code"><![CDATA[ - confil --threads $threads #set $input_type = $input_type_conditional.input_type - #if $input_type == "paired_collection" - --paired - #end if - --cutoff $cutoff + #import re + + ####### Single Input #if $input_type == "single" - "${input_type_conditional.single_input}" + ln -s "${input_type_conditional.single_input}" $input_type_conditional.single_input.element_identifier && + #set report_name = os.path.splitext(os.path.basename($input_type_conditional.single_input.element_identifier))[0] + #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab' + + confil --threads $threads --cutoff $cutoff + $input_type_conditional.single_input.element_identifier + && mv $report_name '$output' + + ####### Paired Collection #elif $input_type == "paired_collection" - "${input_type_conditional.collection_input.forward}" "${input_type_conditional.collection_input.reverse}" + ln -s "${input_type_conditional.collection_input.forward}" $input_type_conditional.collection_input.forward.element_identifier && + ln -s "${input_type_conditional.collection_input.reverse}" $input_type_conditional.collection_input.reverse.element_identifier && + #set report_name = os.path.splitext(os.path.basename($input_type_conditional.collection_input.forward.element_identifier))[0] + #set report_name = re.sub('_[0-9]+$', '', str(report_name)) + '.tab' + + confil --threads $threads --cutoff $cutoff --paired + $input_type_conditional.collection_input.forward.element_identifier $input_type_conditional.collection_input.reverse.element_identifier + && mv $report_name '$output' #end if ]]> </command>