Mercurial > repos > iuc > comebin
diff comebin.xml @ 3:ddfb9c10740a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/comebin/ commit f33c09bd4b736c401cdc037e328c7be4a24d8cf5
| author | iuc |
|---|---|
| date | Thu, 21 Aug 2025 08:48:35 +0000 |
| parents | 15f6ef1d7c96 |
| children |
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--- a/comebin.xml Mon Aug 04 11:21:41 2025 +0000 +++ b/comebin.xml Thu Aug 21 08:48:35 2025 +0000 @@ -11,8 +11,8 @@ mkdir 'outputs' 'bam_files' && - #set $safename = re.sub('[^\w\-_\.]', '_', $assembly_file.element_identifier) - ln -s '$assembly_file' '${safename}.fasta' && + #set $safename_fasta = re.sub('[^\w\-_\.]', '_', $assembly_file.element_identifier) + ln -s '$assembly_file' '${safename_fasta}.fasta' && #for $file in $bam_files: #set $safename = re.sub('[^\w\-_\.]', '_', $file.element_identifier) @@ -20,7 +20,7 @@ #end for run_comebin.sh - -a 'assembly_file.fasta' + -a '${safename_fasta}.fasta' -o 'outputs' -p 'bam_files' -t \${GALAXY_SLOTS:-12} @@ -47,7 +47,7 @@ </collection> </outputs> <tests> - <test expect_exit_code="1" expect_failure="true"> + <test expect_num_outputs="1"> <param name="assembly_file" ftype="fasta" value="input_single.fasta"/> <param name="bam_files" ftype="bam" value="input_single.bam"/> <param name="learning" value="6"/> @@ -81,4 +81,4 @@ ]]> </help> <expand macro="citations"/> -</tool> \ No newline at end of file +</tool>