Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.5.1.0.0 (this tool) |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.3.2.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.3.0.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.2.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.2.0.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.1.2.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.0.2.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.0.1.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_alignmentsieve/deeptools_alignmentsieve/3.0.0.0 |
deeptools_alignmentsieve |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
deeptools | 3.5.1 | package |
samtools | 1.9 | package |
Additional information about this tool |
#import re #set label = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier)) ln -s '$bamfile' one.bam && #if $bamfile.ext == 'bam': ln -s '${bamfile.metadata.bam_index}' one.bam.bai && #else: ln -s '${bamfile.metadata.cram_index}' one.bam.crai && #end if alignmentSieve --numberOfProcessors "\${GALAXY_SLOTS:-4}" -b one.bam --label '$label' #if str($filterRNAstrand) != 'no': --filterRNAstrand '$filterRNAstrand' #end if $ignoreDuplicates #if $minMappingQuality: --minMappingQuality '$minMappingQuality' #end if #if $samFlagInclude: --samFlagInclude $samFlagInclude #end if #if $samFlagExclude: --samFlagExclude $samFlagExclude #end if #if $minFragmentLength: --minFragmentLength $minFragmentLength #end if #if $maxFragmentLength: --maxFragmentLength $maxFragmentLength #end if #if ' '.join( map(str, $blackListFileName) ) != 'None': #set blfiles=[] #for $f in $blackListFileName: #silent $blfiles.append("'%s'" % $f) #end for #if $blfiles != ["'None'"]: --blackListFileName #echo ' '.join($blfiles)# #end if #end if #if $filterMetrics: --filterMetrics '$filterMetricsFile' #end if #if $filteredOutReads: --filteredOutReads '$outFileFiltered' #end if #if str($shift) != "": #set shifts = " ".join(["'{}'".format(x) for x in $shift.split(" ")]) --shift $shifts #elif $ATACshift: --ATACshift #end if #if $BED: --BED -o '$outFile' #elif str($shift) != "" or $ATACshift: -o foo.bam && samtools sort -o '$outFile' -T foo.tmp -@ "\${GALAXY_SLOTS:-4}" foo.bam && rm foo.bam #else: -o '$outFile' #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
bamfile: paired_chr2L.bam minMappingQuality: 10 filterMetrics: True |
name: value name: value |
paired_chr2L.bam value |
Test-2 |
bamfile: paired_chr2L.bam BED: True shift: 1 -2 3 -4 minMappingQuality: 10 |
name: value |
paired_chr2L.bam value |
Test-3 |
bamfile: paired_chr2L.bam shift: 1 -2 3 -4 minMappingQuality: 10 |
name: value |
paired_chr2L.bam value |
Test-4 |
bamfile: paired_chr2L.cram shift: 1 -2 3 -4 minMappingQuality: 10 |
name: value |
paired_chr2L.cram value |