Mercurial > repos > lparsons > freebayes
changeset 2:c70c9dc2efb7
Incorporated changes to suppress stderr messages from samtools calls (borrowed style from galaxy-central tool config)
| author | Lance Parsons <lparsons@princeton.edu> |
|---|---|
| date | Thu, 22 Dec 2011 12:03:14 -0500 |
| parents | 17c497d5826d |
| children | 72bdc513a54a |
| files | freebayes.xml |
| diffstat | 1 files changed, 10 insertions(+), 9 deletions(-) [+] |
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--- a/freebayes.xml Fri Nov 11 17:05:24 2011 -0500 +++ b/freebayes.xml Thu Dec 22 12:03:14 2011 -0500 @@ -12,26 +12,27 @@ exit 2; fi; #if $genomeSource.refGenomeSource == "history": - ln -s "$genomeSource.ownFile" localref.fa; + ln -s "$genomeSource.ownFile" localref.fa && #else: - ln -s "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" localref.fa; + ln -s "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" localref.fa && #end if - samtools faidx localref.fa; + samtools faidx localref.fa 2>&1 || echo "Error running samtools faidx for FreeBayes" >&2 && #if ($params.source_select == "full") and (str($params.baqAdjustment) == 'true') - samtools fillmd -Arb ${bamfile} localref.fa > localbam.bam; + samtools fillmd -Arb ${bamfile} localref.fa > localbam.bam 2>&1 || echo "Error running samtools fillmd for FreeBayes" >&2 && #else - ln -s ${bamfile} localbam.bam; + ln -s ${bamfile} localbam.bam && #end if - samtools index localbam.bam; + + samtools index localbam.bam 2>&1 || echo "Error running samtools index for FreeBayes" >&2 && #for $i, $b in enumerate($bamfiles) #if ($params.source_select == "full") and (str($params.baqAdjustment) == 'true') - samtools fillmd -Arb ${b.additional_bamfile} localref.fa > localbam_${i}.bam; + samtools fillmd -Arb ${b.additional_bamfile} localref.fa > localbam_${i}.bam 2>&1 || echo "Error running samtools fillmd for FreeBayes" >&2 && #else - ln -s ${b.additional_bamfile} localbam_${i}.bam; + ln -s ${b.additional_bamfile} localbam_${i}.bam && #end if - samtools index localbam_${i}.bam; + samtools index localbam_${i}.bam 2>&1 || echo "Error running samtools index for FreeBayes" >&2 && #end for freebayes localbam*.bam --fasta-reference localref.fa --vcf $output