Mercurial > repos > edward-kirton > roche454_toolsuite

comparison roche454/runMapping_wrapper.pl @ 1:368a6ebebdde

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Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author edward-kirton
date Tue, 07 Jun 2011 17:51:04 -0400
parents f036c7107601
children
comparison
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0:f036c7107601 1:368a6ebebdde
6 # EXPECT 21 FILE HANDLES, SOME OF WHICH MAY BE 'None' 6 # EXPECT 21 FILE HANDLES, SOME OF WHICH MAY BE 'None'
7 my $outdir=shift @ARGV; 7 my $outdir=shift @ARGV;
8 my $alignment_info=shift @ARGV; 8 my $alignment_info=shift @ARGV;
9 my $all_contigs_fasta=shift @ARGV; 9 my $all_contigs_fasta=shift @ARGV;
10 my $all_contigs_qual=shift @ARGV; 10 my $all_contigs_qual=shift @ARGV;
11 my $all_diffs=shift @ARGV 11 my $all_diffs=shift @ARGV;
12 my $all_struct_vars=shift @ARGV 12 my $all_struct_vars=shift @ARGV;
13 my $hc_diff=shift @ARGV 13 my $hc_diff=shift @ARGV;
14 my $hc_struct_vars=shift @ARGV 14 my $hc_struct_vars=shift @ARGV;
15 my $mapping_qc=shift @ARGV 15 my $mapping_qc=shift @ARGV;
16 my $newbler_metrics=shift @ARGV; 16 my $newbler_metrics=shift @ARGV;
17 my $pair_align=shift @ARGV; 17 my $pair_align=shift @ARGV;
18 my $read_status=shift @ARGV; 18 my $read_status=shift @ARGV;
19 my $ref_status=shift @ARGV; 19 my $ref_status=shift @ARGV;
20 my $tag_pair_align=shift @ARGV; 20 my $tag_pair_align=shift @ARGV;