Mercurial > repos > iuc > meryl
diff meryl.xml @ 10:f361d6eb1046 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit f09759ed13dd6c6efabbdd79fb171b2d3bfdc927"
| author | iuc |
|---|---|
| date | Thu, 28 Apr 2022 18:10:51 +0000 |
| parents | fb4593698c9e |
| children | c6e9752d4104 |
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--- a/meryl.xml Tue Oct 05 15:57:41 2021 +0000 +++ b/meryl.xml Thu Apr 28 18:10:51 2022 +0000 @@ -77,18 +77,21 @@ #set size=$operation_type.options_kmer_size.input_kmer_size #end if #for $i, $read in enumerate($paternal_reads): - mkdir 'paternal{$i}.meryl' && - meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'paternal{$i}.meryl' && + mkdir 'paternal${i}.meryl' && + ln -s '$read' ./input_paternal_${i}.${read.ext} && + meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_paternal_${i}.${read.ext} output 'paternal${i}.meryl' && #end for meryl union-sum paternal*.meryl output pat.meryl && #for $i, $read in enumerate($maternal_reads): - mkdir 'maternal{$i}.meryl' && - meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'maternal{$i}.meryl' && + mkdir 'maternal${i}.meryl' && + ln -s '$read' ./input_maternal_${i}.${read.ext} && + meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_maternal_${i}.${read.ext} output 'maternal${i}.meryl' && #end for meryl union-sum maternal*.meryl output mat.meryl && #for $i, $read in enumerate($child_reads): - mkdir 'child{$i}.meryl' && - meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} '${read}' output 'child{$i}.meryl' && + mkdir 'child${i}.meryl' && + ln -s '$read' ./input_child_${i}.${read.ext} && + meryl count k=$size memory=\$GALAXY_MEMORY_GB threads=\${GALAXY_SLOTS:-1} ./input_child_${i}.${read.ext} output 'child${i}.meryl' && #end for meryl union-sum child*.meryl output child.meryl && ## mat specific kmers