# HG changeset patch # User greg # Date 1682427587 0 # Node ID 1442e77ee8e9f7ef8674351a8b5a9b9d09d54c73 # Parent 2c61adbbdbdb30d112cc4fb14fc2cdeb9308a35c Uploaded diff -r 2c61adbbdbdb -r 1442e77ee8e9 filter_contigs.xml --- a/filter_contigs.xml Thu Jan 26 16:17:43 2023 +0000 +++ b/filter_contigs.xml Tue Apr 25 12:59:47 2023 +0000 @@ -1,4 +1,4 @@ - + from an assembled FASTA file macros.xml @@ -10,11 +10,27 @@ #else: ln -s '$input' 'input.fasta' && #end if -faidx -i chromsizes 'input.fasta' | awk '($2 <= $max_len) {print $1}' | parallel -n1 -n1 \$(which faidx) 'input.fasta' > '$output' +#if str($max_min_cond.max_min) == 'max': + faidx -i chromsizes 'input.fasta' | awk '($2 <= $max_min_cond.max_len) {print $1}' | parallel -n1 -n1 \$(which faidx) 'input.fasta' > '$output' +#else: + faidx -i chromsizes 'input.fasta' | awk '($2 > $max_min_cond.min_len) {print $1}' | parallel -n1 -n1 \$(which faidx) 'input.fasta' > '$output' +#end if + ]]> - + + + + + + + + + + + +