Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.4+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.2+galaxy0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.5.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.2.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.3.0.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.2.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.2.0.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.1.2.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.2.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.1.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/3.0.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.7.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.1.1.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.5.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.4.2.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.4.1.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.3.6.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.3.5.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.3.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.2.2.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_bam_coverage/deeptools_bam_coverage/2.0.1.0 |
deeptools_bam_coverage |
Requirements (dependencies defined in the <requirements> tag set) |
name | version | type |
deeptools | 3.5.4 | package |
samtools | 1.9 | package |
Additional information about this tool |
ln -s '$bamInput' one.bam && #if $bamInput.ext == 'bam': ln -s '${bamInput.metadata.bam_index}' one.bam.bai && #else: ln -s '${bamInput.metadata.cram_index}' one.bam.crai && #end if bamCoverage --numberOfProcessors "\${GALAXY_SLOTS:-4}" --bam one.bam --outFileName '$outFileName' --outFileFormat '$outFileFormat' --binSize $binSize #if $scaling.type=='rpkm': --normalizeUsing RPKM #elif $scaling.type=='cpm': --normalizeUsing CPM #elif $scaling.type=='bpm': --normalizeUsing BPM #elif $scaling.type=='1x': --normalizeUsing RPGC #if $scaling.effectiveGenomeSize.effectiveGenomeSize_opt == "specific": --effectiveGenomeSize $scaling.effectiveGenomeSize.effectiveGenomeSize #else: --effectiveGenomeSize $scaling.effectiveGenomeSize.effectiveGenomeSize_opt #end if #end if #if str($region).strip() != '': --region '$region' #end if $exactScaling #if $advancedOpt.showAdvancedOpt == "yes": #if str($advancedOpt.scaleFactor).strip() != '': --scaleFactor $advancedOpt.scaleFactor #end if #if $advancedOpt.smoothLength: --smoothLength '$advancedOpt.smoothLength' #end if #if $advancedOpt.doExtendCustom.doExtend == 'custom': --extendReads $advancedOpt.doExtendCustom.extendReadsValue #else if $advancedOpt.doExtendCustom.doExtend == 'yes': --extendReads #end if $advancedOpt.ignoreDuplicates $advancedOpt.centerReads #if $advancedOpt.minMappingQuality: --minMappingQuality '$advancedOpt.minMappingQuality' #end if #if $advancedOpt.samFlagInclude: --samFlagInclude $advancedOpt.samFlagInclude #end if #if $advancedOpt.samFlagExclude: --samFlagExclude $advancedOpt.samFlagExclude #end if #if $advancedOpt.minFragmentLength: --minFragmentLength $advancedOpt.minFragmentLength #end if #if $advancedOpt.maxFragmentLength: --maxFragmentLength $advancedOpt.maxFragmentLength #end if $advancedOpt.skipNAs #if str($advancedOpt.ignoreForNormalization).strip() != '': --ignoreForNormalization $advancedOpt.ignoreForNormalization #end if #if str($advancedOpt.filterRNAstrand) != 'no': --filterRNAstrand '$advancedOpt.filterRNAstrand' #end if #if $advancedOpt.Offset: --Offset $advancedOpt.Offset #end if #if ' '.join( map(str, $advancedOpt.blackListFileName) ) != 'None': #set blfiles=[] #for $f in $advancedOpt.blackListFileName: #silent $blfiles.append("'%s'" % $f) #end for #if $blfiles != ["'None'"]: --blackListFileName #echo ' '.join($blfiles)# #end if #end if #end if
Functional tests |
name | inputs | outputs | required files |
Test-1 |
bamInput: bowtie2 test1.bam binSize: 10 scaling|type: no outFileFormat: bigwig advancedOpt|showAdvancedOpt: no |
name: value |
bowtie2 test1.bam value |
Test-2 |
bamInput: bowtie2 test1.bam binSize: 10 scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000 scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific outFileFormat: bigwig advancedOpt|showAdvancedOpt: no |
name: value |
bowtie2 test1.bam value |
Test-3 |
bamInput: bowtie2 test1.bam binSize: 10 scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000 scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific outFileFormat: bedgraph advancedOpt|showAdvancedOpt: no |
name: value |
bowtie2 test1.bam value |
Test-4 |
bamInput: phiX.bam binSize: 10 scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000 scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific outFileFormat: bigwig advancedOpt|showAdvancedOpt: no |
name: value |
phiX.bam value |
Test-5 |
bamInput: phiX.bam binSize: 10 scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000 scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific outFileFormat: bedgraph advancedOpt|showAdvancedOpt: yes |
name: value |
phiX.bam value |
Test-6 |
bamInput: phiX.bam binSize: 10 scaling|effectiveGenomeSize|effectiveGenomeSize: 2451960000 scaling|effectiveGenomeSize|effectiveGenomeSize_opt: specific outFileFormat: bigwig advancedOpt|filterRNAstrand: reverse advancedOpt|showAdvancedOpt: yes |
name: value |
phiX.bam value |
Test-7 |
bamInput: bowtie2 test1.bam binSize: 10 scaling|type: no outFileFormat: bigwig advancedOpt|doExtendCustom|doExtend: yes advancedOpt|minMappingQuality: 0 advancedOpt|Offset: -4 -1 advancedOpt|showAdvancedOpt: yes |
name: value |
bowtie2 test1.bam value |