Miscellaneous |
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
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 |