Miscellaneous |
Version lineage of this tool (guids ordered most recent to oldest) |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.4+galaxy0 (this tool) |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.2+galaxy0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.5.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.2.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.3.0.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.2.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.2.0.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.1.2.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.2.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.1.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/3.0.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.5.7.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.5.1.1.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.5.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.5.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.4.2.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.4.1.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.3.6.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.3.5.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.2.3.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.2.2.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.1.0.0 |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_plot_coverage/deeptools_plot_coverage/2.0.1.0 |
deeptools_plot_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 |
#set files=[] #set labels=[] #if $custom_sample_labels_conditional.custom_labels_select == "Yes": #set custom_labels=$custom_sample_labels_conditional.labels #end if #set files=[] #set labels=[] #import re #if $multibam_conditional.orderMatters == "No": #for $counter, $bamfile in enumerate($multibam_conditional.bamfiles): #set identifier = re.sub('[^\.\s\w\-]', '_', str($bamfile.element_identifier)) ln -s '${bamfile}' './${counter}.bam' && #if $bamfile.ext == 'bam': ln -s '${bamfile.metadata.bam_index}' './${counter}.bam.bai' && #else: ln -s '${bamfile.metadata.cram_index}' './${counter}.bam.crai' && #end if #silent $files.append("'%s.bam'" % $counter) #silent $labels.append("'%s'" % $identifier) #end for #else: #for $counter, $f in enumerate($multibam_conditional.multibam_repeats): #set identifier = re.sub('[^\.\s\w\-]', '_', str($f.bamfiles.element_identifier)) ln -s '${f.bamfiles}' './${counter}.bam' && #if $f.bamfiles.ext == 'bam': ln -s '${f.bamfiles.metadata.bam_index}' './${counter}.bam.bai' && #else: ln -s '${f.bamfiles.metadata.cram_index}' './${counter}.bam.crai' && #end if #silent $files.append("'%s.bam'" % $counter) #silent $labels.append("'%s'" % $identifier) #end for #end if #if $custom_sample_labels_conditional.custom_labels_select == "Yes": #set labels=custom_labels #end if plotCoverage --numberOfProcessors "\${GALAXY_SLOTS:-4}" --plotFile '$outFileName' --bamfiles #echo " ".join($files)# --labels #echo " ".join($labels)# --plotFileFormat '$outFileFormat' #if $outRawCounts: --outRawCounts '$outFileRawCounts' #end if #if ' '.join(map(str, $BED)) != 'None': #set bedFileList=[] #for $f in $BED: #silent $bedFileList.append("'%s'" % $f) #end for #if $bedFileList != ["'None'"]: --BED #echo ' '.join($bedFileList)# #end if #end if #if $coverageOpt.showCoverageOpt == "yes": --outCoverageMetrics '$outFileCoverageMetrics' #for $t in $coverageOpt.thresholds: -ct $t.coverageThreshold #end for #end if #if $advancedOpt.showAdvancedOpt == "yes": --numberOfSamples '$advancedOpt.numberOfSamples' $advancedOpt.skipZeros #if str($advancedOpt.region).strip() != '': --region '$advancedOpt.region' #end if --numberOfSamples $advancedOpt.numberOfSamples #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "": --plotTitle '$advancedOpt.plotTitle' #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 $advancedOpt.maxFragmentLength #end if --plotWidth '$advancedOpt.plotWidth' --plotHeight '$advancedOpt.plotHeight' #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 |
multibam_conditional|bamfiles: ['bowtie2 test1.bam', 'bowtie2 test1.bam'] advancedOpt|plotTitle: Test Title from Galaxy advancedOpt|showAdvancedOpt: yes outRawCounts: True |
name: value name: value |
bowtie2 test1.bam value |
Test-2 |
multibam_conditional|bamfiles: ['bowtie2 test1.bam', 'bowtie2 test1.bam'] coverageOpt|thresholds_0|coverageThreshold: 20 coverageOpt|thresholds_1|coverageThreshold: 10 coverageOpt|thresholds_2|coverageThreshold: 5 coverageOpt|thresholds_3|coverageThreshold: 0 coverageOpt|showCoverageOpt: yes advancedOpt|plotTitle: Test Title from Galaxy advancedOpt|showAdvancedOpt: yes |
name: value name: value |
bowtie2 test1.bam value |