Mercurial > repos > tiagoantao > barcode_stacks
changeset 6:5cd3cc89bf59 draft
planemo upload commit 80e74122bff9cbc1d172f920b164d6db9c028e7b
| author | tiagoantao |
|---|---|
| date | Tue, 29 Mar 2016 12:45:39 -0400 |
| parents | 323f30038a77 |
| children | 2c843c8df821 |
| files | barcode_sort.pl barcode_sort.xml |
| diffstat | 2 files changed, 6 insertions(+), 4 deletions(-) [+] |
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--- a/barcode_sort.pl Tue Mar 29 12:08:53 2016 -0400 +++ b/barcode_sort.pl Tue Mar 29 12:45:39 2016 -0400 @@ -8,6 +8,10 @@ # note this is the length of what's left after enzyme digestion, NOT the full length of the enzyme recognition site # the program expects all correct forward reads to follow the pattern: $n initial nucleotides, then $b nucleotides of barcode, then $e nucleotides of the cutsite +my $is_resilient; + +$is_resilient = $ARGV[5]; # true if is resilient to errors + open (IN, $ARGV[0]); # read file with barcodes my %counts = (); # make a hash of barcodes that will be searched while(<IN>) { # counts of each barcode can be tracked with this hash, with a few more lines of code below
--- a/barcode_sort.xml Tue Mar 29 12:08:53 2016 -0400 +++ b/barcode_sort.xml Tue Mar 29 12:45:39 2016 -0400 @@ -1,7 +1,5 @@ -<tool id="barcode_sort_stacks" name="Barcode sorting for Stacks" version="1.0.0" force_history_refresh="True"> - <description>Run the STACKS populations program</description> - - +<tool id="barcode_sort_stacks" name="Barcode sorting for Stacks" version="1.0.1" force_history_refresh="True"> + <description>Barcode Sorting with Paired-End reads for Stacks</description> <stdio> <exit_code range="1" level="fatal" description="Error in script execution" />