Repository revision
7:5a26589d95ad

Repository 'slamdunk'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/slamdunk

Slamdunk tool metadata
Miscellaneous
Slamdunk
- streamlining SLAM-seq analysis with ultra-high sensitivity
slamdunk
toolshed.g2.bx.psu.edu/repos/iuc/slamdunk/slamdunk/0.4.3+galaxy1
0.4.3+galaxy1
slamdunk --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/slamdunk/slamdunk/0.4.3+galaxy1 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/slamdunk/slamdunk/0.3.3
slamdunk
Requirements (dependencies defined in the <requirements> tag set)
name version type
slamdunk 0.4.3 package
Additional information about this tool
#import re

mkdir fastq &&
#set $reads_id = re.sub('[^\w\-\.]', '_', str($reads.element_identifier))
ln -s '$reads' './fastq/$reads_id' &&

#if $reference_source.reference_source_selector == 'history':
    ln -f -s '$reference_source.ref_file' reference.fa &&
#else:
    ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
#end if

    slamdunk all -r reference.fa -b '$reference' -o ./out
       -t \${GALAXY_SLOTS:-1}
       -n $multimapper.multimappers
        $multimapper.multimap
        #if $multimapper.filterbed.bedtofilter:
            -fb $multimapper.filterbed.bedtofilter
        #end if
        -5 $quantseq.trim5
        -a $quantseq.maxpolyA
        $advanced.endtoend
        -mq $advanced.minMQ
        -mi $advanced.minID
        -nm=$advanced.maxNM
        -mc $advanced.minCov
        -mv $advanced.minVar
        -mbq $advanced.minBaseQual
        -rl $readLength
        -c $covThresh
        #if $advanced.vcf
            --vcf $advanced.vcf
        #end if
        './fastq/$reads_id'

        && mv out/filter/*_slamdunk_mapped_filtered.bam '$outputBam'
        && mv out/count/*_slamdunk_mapped_filtered_tcount.tsv '$outputTsv'
        #if not $advanced.vcf
            && mv out/snp/*_slamdunk_mapped_filtered_snp.vcf '$outputVcf'
        #end if
    
None
False
Functional tests
name inputs outputs required files
Test-1 reference_source|ref_file: ref.fa
reference_source|reference_source_selector: history
reference: actb.bed
reads: reads.fq
quantseq|trim5: 0
advanced|minBaseQual: 27
readLength: 100
name: value
name: value
name: value
ref.fa
actb.bed
reads.fq
value
Test-2 reference_source|ref_file: hg38full
reference_source|reference_source_selector: cached
reference: actb.bed
reads: reads.fq
quantseq|trim5: 0
advanced|minBaseQual: 27
readLength: 100
name: value
name: value
name: value
actb.bed
reads.fq
value
Test-3 reference_source|ref_file: ref.fa
reference_source|reference_source_selector: history
reference: actb.bed
reads: reads.fq
quantseq|trim5: 0
advanced|minBaseQual: 27
advanced|vcf: reads_slamdunk_mapped_filtered_snp.vcf
readLength: 100
name: value
name: value
ref.fa
actb.bed
reads.fq
reads_slamdunk_mapped_filtered_snp.vcf
value