comparison bowtie2_wrapper.xml @ 32:d5ceb9f3c25b draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 7c23f328dedbbf24693ddfcc4ebc6b5ee1801767

31:0d4acadabb04

        #set read1 = "input_f.fastq"
    #end if
    ln -f -s '${library.input_1}' ${read1} &&
#end if

## execute bowtie2

bowtie2

## number of threads
-p \${GALAXY_SLOTS:-4}

## index file path
-x '$index_path'

## Input reads are fasta?

    ${sam_options.reorder}
#end if

## mapping stats (i.e. stderr from bowtie2)
#if $save_mapping_stats
    2> '$mapping_stats'
#end if

## output file
#if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
    | samtools sort --no-PG -@\${GALAXY_SLOTS:-2} -T "\${TMPDIR:-.}" -O bam -o '$output'
#else if $sam_options.reorder:
    | samtools view --no-PG -bS - -o '$output'
#else:
    > '$output'
#end if

## rename unaligned sequence files

32:d5ceb9f3c25b

        #set read1 = "input_f.fastq"
    #end if
    ln -f -s '${library.input_1}' ${read1} &&
#end if


## compute number of threads to be used for bowtie2
## the bowtie parameter -p specifies the number of alignment threads to use (in
## addition to a control thread) # just using GALAXY_SLOTS will lead to
## overcommiting ressources (in particular because there may be a samtools sort or view
## running in parallel). 
## for now we use one thread less than GALAXY_SLOTS
THREADS=\${GALAXY_SLOTS:-4} &&
if [ "\$THREADS" -gt 1 ]; then (( THREADS-- )); fi &&

## execute bowtie2

bowtie2

## number of threads
-p "\$THREADS"

## index file path
-x '$index_path'

## Input reads are fasta?

    ${sam_options.reorder}
#end if

## mapping stats (i.e. stderr from bowtie2)
#if $save_mapping_stats
    2> >(tee '$mapping_stats' >&2) 
#end if

## output file
#if str( $sam_options.sam_options_selector ) == "no" or (str( $sam_options.sam_opt ) == "false" and str($sam_options.reorder) == ''):
    ## Convert SAM output to sorted BAM
    ## using the two pipe stages has the following effect
    ## - mapping and sorting run in parallel, during this time sort produces
    ##   presorted temporary files but does not produce output (hence
    ##   view does not run)
    ## - once mapping is finished sort will start to merge the temporary
    ##   files (which should be fast also on a single thread) gives the
    ##   sorted output to view which only compresses the files (now
    ##   using full parallelism again)
    | samtools sort -l 0 -T "\${TMPDIR:-.}" -O bam | samtools view --no-PG -O bam -@ \${GALAXY_SLOTS:-1} -o '$output'
#else if $sam_options.reorder:
    | samtools view --no-PG -b -o '$output' 
#else:
    > '$output'
#end if

## rename unaligned sequence files