Hello,
I have added a tool in my local instance to map BAM files on reference genome fasta file thanks to BWA. This tool runs, and the output file generated in database/files/000 is correct (not empty and good data inside) but the output listed in the history panel of Galaxy interface , is empty. Could you please help me ?
Here is my xml file:
<tool id="BWA_aln_sampe" name=" BWA with BAM files"> <description>BWA mapping BAM files on reference genome fasta file</description> <command interpreter="perl">bwa_aln_sampe.pl $input1 $input2 $output1 </command> <inputs> <param format="fasta" name="input1" type="data" label="Reference genome from your history - fasta file"/> <param format="bam" name="input2" type="data" label="Bam file"/> </inputs> <outputs> <data format="bam" name="output1" /> </outputs>
<help> This tool map BAM files on a reference genome. </help>
</tool>
Here is my perl file : #!/usr/bin/perl -w use strict; use File::Basename;
my $input_ref_genome = $ARGV[0]; my $input_bam = $ARGV[1]; my $output_bam = $ARGV[2]; my $input_dir=dirname($input_bam); my $input_basename=basename($input_bam,'.bam'); my $input_bamsorted="$input_dir/${input_basename}-sorted";
#Ouverture des fichiers entrants open (IN, "<$input_ref_genome") or die "Cannot open $input_ref_genome !"; open (IN, "<$input_bam") or die "Cannot open $input_bam !";
#Indexation du genome de reference #system("bwa index $input_ref_genome >> ./bwa.log 2>&1");
#Tri par nom du bam entrant pour travailler sur des donnees pairees system("samtools sort -n $input_bam $input_bamsorted >> ./samtools.log 2>&1");
#Alignement des donnees pairees uniquement system("bwa aln $input_ref_genome -b1 ${input_bamsorted}.bam > ${input_bamsorted}-1.sai >> ./bwaaln.log 2>&1"); system("bwa aln $input_ref_genome -b2 ${input_bamsorted}.bam > ${input_bamsorted}-2.sai >> ./bwaaln.log 2>&1");
#bwa sampe system("bwa sampe $input_ref_genome ${input_bamsorted}-1.sai ${input_bamsorted}-2.sai ${input_bamsorted}.bam ${input_bamsorted}.bam | samtools view -bS - > $output_bam >> ./bwa.log 2>&1");
close( IN ); close( IN );
Thanks in advance, Sarah