Repository revision
11:bddbd9538b08

Repository 'deeptools_estimatereadfiltering'
hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering

estimateReadFiltering tool metadata
Miscellaneous
estimates the number of reads that would be filtered given certain criteria
deeptools_estimatereadfiltering
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.5.2+galaxy0
3.5.2+galaxy0
estimateReadFiltering --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_estimatereadfiltering/deeptools_estimatereadfiltering/3.0.0.0
deeptools_estimatereadfiltering
Requirements (dependencies defined in the <requirements> tag set)
name version type
deeptools 3.5.2 package
samtools 1.9 package
Additional information about this tool
#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

    
        estimateReadFiltering
        --numberOfProcessors "\${GALAXY_SLOTS:-4}"

        -o '$outFileName'

        --bamfiles #echo " ".join($files)#
        --sampleLabels #echo " ".join($labels)#

        -bs '$binSize'
        --distanceBetweenBins '$distanceBetweenBins'

        #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 ' '.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

    
None
False
Functional tests
name inputs outputs required files
Test-1 multibam_conditional|bamfiles: ['paired_chr2L.bam', 'paired_chr2L.bam']
minMappingQuality: 10
name: value
paired_chr2L.bam
value