Mercurial > repos > portiahollyoak > temp
changeset 11:e19d9742c99b draft
planemo upload for repository https://github.com/portiahollyoak/Tools commit bfcc36291d97d1c0986f034ca1a03433e8299ff2-dirty
| author | portiahollyoak |
|---|---|
| date | Thu, 28 Apr 2016 07:57:12 -0400 |
| parents | 3200a0299230 |
| children | ca36262102d8 |
| files | scripts/pickUniqPairFastq.pl scripts/pickUniqPos.pl temp.xml |
| diffstat | 3 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/scripts/pickUniqPairFastq.pl Wed Apr 27 11:44:13 2016 -0400 +++ b/scripts/pickUniqPairFastq.pl Thu Apr 28 07:57:12 2016 -0400 @@ -21,7 +21,7 @@ ## revcom the read mapped to the reverse strand if($f[1]=~/r/) { - my $seq=Bio::Seq->new(-seq=>$f[9]); + my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna'); $f[9]=$seq->revcom->seq; $f[10]=reverse $f[10]; }
--- a/scripts/pickUniqPos.pl Wed Apr 27 11:44:13 2016 -0400 +++ b/scripts/pickUniqPos.pl Thu Apr 28 07:57:12 2016 -0400 @@ -19,7 +19,7 @@ ## revcomp if($f[1]=~/r/) { - my $seq=Bio::Seq->new(-seq=>$f[9]); + my $seq=Bio::Seq->new(-seq=>$f[9], -alphabet => 'dna'); $f[9]=$seq->revcom->seq; $strand="-"; }
--- a/temp.xml Wed Apr 27 11:44:13 2016 -0400 +++ b/temp.xml Thu Apr 28 07:57:12 2016 -0400 @@ -20,7 +20,7 @@ ln -f -s "$alignment.metadata.bam_index" alignment.sorted.bam.bai && ln -f -s "$alignment" alignment.sorted.bam && - bash $__tool_directory__/scripts/TEMP_Insertion.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && + bash $__tool_directory__/scripts/TEMP_Insertion.sh -x 30 -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$consensus_te_seqs" -t "$bed_te_locations" -m 3 -f "$median_insertsize" -c \${GALAXY_SLOTS:-2} && bash $__tool_directory__/scripts/TEMP_Absence.sh -i alignment.sorted.bam -s $__tool_directory__/scripts -r "$bed_te_locations" -t "$reference2bit" -f 500 -c \${GALAXY_SLOTS:-2} && mv alignment.insertion.bp.bed $insertion_bed && mv alignment.insertion.refined.bp $insertion_bed_refined &&