Mercurial > repos > devteam > cuffquant
diff cuffquant_wrapper.xml @ 2:b2ee2bef1926 draft
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/cufflinks/cuffquant commit eb18f691975ef9539b5ebd4f118343c8ad967a1f
author | devteam |
---|---|
date | Tue, 07 Feb 2017 18:40:42 -0500 |
parents | 986b63735a5e |
children | 6dc45faebc1d |
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--- a/cuffquant_wrapper.xml Wed Nov 11 12:35:31 2015 -0500 +++ b/cuffquant_wrapper.xml Tue Feb 07 18:40:42 2017 -0500 @@ -1,11 +1,11 @@ <tool id="cuffquant" name="Cuffquant" version="@VERSION@.0"> <!-- Wrapper supports Cuffdiff versions 2.2.1 --> <description>Precompute gene expression levels</description> - <expand macro="requirements" /> - <expand macro="stdio" /> <macros> <import>cuff_macros.xml</import> </macros> + <expand macro="requirements" /> + <expand macro="stdio" /> <version_command>cuffquant 2>&1 | head -n 1</version_command> <command> cuffquant @@ -27,10 +27,10 @@ -b #if $bias_correction.seq_source.index_source == "history": ## Custom genome from history. - $bias_correction.seq_source.ref_file + '$bias_correction.seq_source.ref_file' #else: ## Built-in genome. - "${ bias_correction.seq_source.index.fields.path }" + '${bias_correction.seq_source.index.fields.path}' #end if #end if @@ -42,15 +42,15 @@ --library-type=$advanced_settings.library_type #end if #if $advanced_settings.mask_file: - --mask-file=$advanced_settings.mask_file + --mask-file '$advanced_settings.mask_file' #end if --max-mle-iterations=$advanced_settings.max_mle_iterations --max-bundle-frags=$advanced_settings.max_bundle_frags #end if ## Inputs. - $gtf_input + '$gtf_input' #set samplestring = ','.join( [ str( $sample.sample ) for $sample in $samples ] ) - $samplestring + '$samplestring' </command> <inputs> <param format="gtf,gff3" name="gtf_input" type="data" label="Transcripts"