echo Mapping reads with clc_mapper...
&& \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_mapper
#for $ref in $references
#if str($ref.ref_type)=="circular"
-d -z '$ref.ref_file'
#else
-d '$ref.ref_file'
#end if
#end for
#for $rg in $read_group
##--------------------------------------
#if str($rg.segments.type) == "paired"
-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q -i '$rg.segments.filename1' '$rg.segments.filename2'
#end if
##--------------------------------------
#if str($rg.segments.type) == "interleaved"
-p $rg.segments.placement $rg.segments.dist_mode $rg.segments.min_size $rg.segments.max_size -q '$rg.segments.filename'
#end if
##--------------------------------------
#if str($rg.segments.type) == "none"
-p no -q
#for $f in $rg.segments.filenames
'$f'
#end for
#end if
##--------------------------------------
#end for
-o "temp_job.cas"
--cpus "\${GALAXY_SLOTS:-4}"
## TODO - filtering out the progress lines seems to mess up the multiple commands
## | grep -v "^Progress: "
##===========================================
## TODO - I've required all the input in Sanger FASTQ format (or FASTA) so can
## use the offset 33, rather then the CLCbio default of 64 which is only for
## obsolete Illumina FASTQ files. Really need this option per input file...
&& echo Converting CAS file to BAM with clc_cas_to_sam...
&& \${CLC_ASSEMBLY_CELL:-/mnt/apps/clcBio/clc-assembly-cell-4.1.0-linux_64/}clc_cas_to_sam --cas 'temp_job.cas' -o 'temp_job.bam' --no-progress --qualityoffset 33
#if $discard_unmapped:
## -u / --discardunmapped: Discard the unmapped reads
-u
#end if
&& rm 'temp_job.cas'
##===========================================
&& echo Sorting BAM file with samtools...
&& samtools sort "temp_job.bam" "temp_sorted"
&& mv "temp_sorted.bam" "$out_bam"
&& echo Indexing BAM file with samtools...
&& samtools index "$out_bam"