Mercurial > repos > devteam > cuffmerge
diff cuffmerge_wrapper.xml @ 14:6a6717a5f421 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/cufflinks/cuffmerge commit a0b0845a9d1b3e7ecdeacd1e606133617e3918bd"
author | iuc |
---|---|
date | Tue, 16 Jun 2020 13:00:53 -0400 |
parents | cf747d1bd79a |
children | 86285ddd4512 |
line wrap: on
line diff
--- a/cuffmerge_wrapper.xml Sun Feb 19 12:12:38 2017 -0500 +++ b/cuffmerge_wrapper.xml Tue Jun 16 13:00:53 2020 -0400 @@ -1,14 +1,16 @@ -<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.1"> +<tool id="cuffmerge" name="Cuffmerge" version="@VERSION@.2"> <description>merge together several Cufflinks assemblies</description> <macros> <import>cuff_macros.xml</import> </macros> <expand macro="requirements" /> - <version_command>cuffmerge -v</version_command> - <command detect_errors="aggressive"> - python '$__tool_directory__/cuffmerge_wrapper.py' + <version_command>cuffmerge -v</version_command> + <command detect_errors="aggressive"><![CDATA[ + @CUFFLINKS_LINK_GTF_INPUTS@ + echo @CUFFLINKS_GTF_INPUTS@ | sed 's/\s\+/\n/' > assembly_GTF_list.txt && + cuffmerge + -o output --num-threads="\${GALAXY_SLOTS:-4}" - ## Use annotation reference? #if $annotation.use_ref_annotation == "Yes": -g '${annotation.reference_annotation}' @@ -25,12 +27,8 @@ #end if --min-isoform-fraction="${min_isoform_fraction}" - - ## Outputs. - --merged-transcripts '${merged_transcripts}' - - @CUFFLINKS_GTF_INPUTS@ - </command> + assembly_GTF_list.txt + ]]></command> <inputs> <expand macro="cufflinks_gtf_inputs" /> <conditional name="annotation"> @@ -74,7 +72,7 @@ </inputs> <outputs> - <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts"/> + <data format="gtf" name="merged_transcripts" label="${tool.name} on ${on_string}: merged transcripts" from_work_dir="output/merged.gtf"/> </outputs> <tests> @@ -127,7 +125,5 @@ Cuffmerge produces a GTF file that contains an assembly that merges together the input assemblies. </help> - <citations> - <citation type="doi">10.1038/nbt.1621</citation> - </citations> + <expand macro="citations"/> </tool>