Mercurial > repos > jtilman > flexbar

changeset 35:cb6423bc1097 draft

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Deleted selected files
author jtilman
date Wed, 27 Jun 2018 06:42:25 -0400
parents 4a095317caca
children 4e47e1caf21a
files flexbar.pl
diffstat 1 files changed, 0 insertions(+), 34 deletions(-) [+]
line wrap: on
line diff
--- a/flexbar.pl	Wed Jun 27 06:41:36 2018 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,34 +0,0 @@
-#!/usr/bin/env perl
-
-# Flexbar wrapper for Galaxy tool definition, version 3.4
-# Author: Johannes Roehr
-
-use warnings;
-use strict;
-
-my ($outFile, $id, $folder, $format) = @ARGV[($#ARGV - 3) .. $#ARGV];
-
-my $call = join " ", @ARGV[0..($#ARGV - 4)];
-
-system $call .' --target FlexbarTargetFile --output-log '. $outFile and exit 1;
-
-
-foreach(<FlexbarTargetFile*>){
-	
-	my $fileType;
-	
-	$fileType = $1         if /\.(\w+)$/;
-	$fileType = $format    if /\.\w*fast\w$/;
-	$fileType = 'fasta'    if /\.fasta$/;
-	$fileType = 'tabular'  if /\.lengthdist$/;
-	
-	my $file = $_;
-	
-	s/_/-/g;
-	
-	my $name = "primary_". $id ."_". $_ ."_visible_". $fileType;
-	
-	rename $file, $name;
-	rename $name, $folder;
-}
-