Mercurial > repos > mcharles > rapsodyn
changeset 2:428799b67007 draft
Uploaded
| author | mcharles |
|---|---|
| date | Mon, 16 Jun 2014 06:11:14 -0400 |
| parents | 2e27d068d9b0 |
| children | e29e077a1674 |
| files | filtersamunique/filtersamunique.pl filtersamunique/filtersamunique.xml filtersamunique/test.tar.bz2 |
| diffstat | 3 files changed, 38 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filtersamunique/filtersamunique.pl Mon Jun 16 06:11:14 2014 -0400 @@ -0,0 +1,20 @@ +#!/usr/bin/perl +use strict; +use warnings; + +open(IN, $ARGV[0]) or die ("Can't open $ARGV[0]\n"); +while (my $line=<IN>){ + if ($line =~ /^\@/){ + #Header conservation + print $line; + } + else { + #Optionnal flag verification + if (($line =~ /XT\:A\:U/)&&($line =~ /X0\:i\:1/)&&($line =~ /X1\:i\:0\s/)){ + print $line; + } + } +} + + +close (IN); \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/filtersamunique/filtersamunique.xml Mon Jun 16 06:11:14 2014 -0400 @@ -0,0 +1,18 @@ +<tool id="filtersamunique" name="filtersamunique" version="0.01"> +<description>Filter SAM file for uniquelly match reads</description> +<command interpreter="perl"> + filtersamunique.pl $input_sam_file > $output_file +</command> +<inputs> +<param name="input_sam_file" type="data" format="sam" label="Select a suitable input SAM file from your history"/> +</inputs> +<outputs> + <data name="output_file" format="sam" label="${tool.name} on ${on_string}"/> +</outputs> + +<help> + + + +</help> +</tool>