Mercurial > repos > thanhlv > canu
changeset 5:414a7cecc8e9 draft default tip
"planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/canu commit 4edfce31568e499b12a8e41fecc9329f7ae42055-dirty"
| author | thanhlv |
|---|---|
| date | Wed, 02 Feb 2022 20:05:45 +0000 |
| parents | 7aebd87ded84 |
| children | |
| files | canu.xml |
| diffstat | 1 files changed, 16 insertions(+), 14 deletions(-) [+] |
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--- a/canu.xml Wed Feb 02 19:11:26 2022 +0000 +++ b/canu.xml Wed Feb 02 20:05:45 2022 +0000 @@ -13,14 +13,22 @@ GALAXY_MEMORY_GB=\$((GALAXY_MEMORY_MB / 1024)) ; fi ; - #if $input.ext in ['fastq.gz', 'fasta.gz', 'fastqsanger.gz'] - ## linking does not work - cp '$input' ./input.gz && - else if $input.ext in ['fastq', 'fastqsanger'] - cp '$input' ./input.fastq && - else if $input.ext in ['fasta'] - cp '$input' ./input.fasta && + #if $input.is_of_type('fastqsanger', 'fastq'): + #set $ext = 'fastq' + #elif $input.is_of_type('fastqsanger.gz'): + #set $ext = 'fastq.gz' + #elif $input.is_of_type('fastq'): + #set $ext = 'fastq' + #elif $input.is_of_type('fastq.gz'): + #set $ext = 'fastq.gz' + #elif $input.is_of_type('fasta.gz'): + #set $ext = 'fasta.gz' + #elif $input.is_of_type('fasta'): + #set $ext = 'fasta' #end if + + cp $input ./input.${ext} && + canu #if $stage != 'all': $stage @@ -58,13 +66,7 @@ cnsThreads=\${GALAXY_SLOTS:-4} useGrid=false $mode - #if $input.ext in ['fastq.gz', 'fasta.gz', 'fastqsanger.gz'] - ./input.gz && - else if $input.ext in ['fastq', 'fastqsanger'] - ./input.fastq && - else if $input.ext in ['fasta'] - ./input.fasta && - #end if + ./input.${ext} 2>&1 && echo "Check echo"