Repository revision
8:21d859ad4502

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

hicQuickQC tool metadata
Miscellaneous
hicQuickQC
get a first quality estimate of Hi-C data
hicexplorer_hicquickqc
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicquickqc/hicexplorer_hicquickqc/3.7.2+galaxy0
3.7.2+galaxy0
hicQuickQC --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicquickqc/hicexplorer_hicquickqc/3.7.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicquickqc/hicexplorer_hicquickqc/3.6+galaxy1
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicquickqc/hicexplorer_hicquickqc/3.6+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicquickqc/hicexplorer_hicquickqc/3.4.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicquickqc/hicexplorer_hicquickqc/3.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicquickqc/hicexplorer_hicquickqc/3.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hicquickqc/hicexplorer_hicquickqc/3.3.1.0
hicexplorer_hicquickqc
Requirements (dependencies defined in the <requirements> tag set)
name version type
hicexplorer 3.7.2 package
Additional information about this tool
mkdir ./QCfolder &&
        mkdir $qc.files_path &&
        hicQuickQC

            --samFiles
            #for $repeat in $samFiles:
                '${repeat.samFile}'
            #end for

            --restrictionCutFile '$restrictionCutFile'
            
            #if $restrictionSequence:
                --restrictionSequence '$restrictionSequence'
            #end if

            #if $danglingSequence:
                --danglingSequence '$danglingSequence'
            #end if
            --QCfolder ./QCfolder

            --lines $lines

        && mv ./QCfolder/* $qc.files_path/
        && mv $qc.files_path/hicQC.html $qc
        && mv $qc.files_path/*.log raw_qc
        
None
False
Functional tests
name inputs outputs required files
Test-1 samFiles_0|samFile: small_test_R1_unsorted.sam
samFiles_1|samFile: small_test_R2_unsorted.sam
restrictionCutFile: DpnII_10k.bed
restrictionSequence: GATC
danglingSequence: GATC
lines: 1000
name: value
small_test_R1_unsorted.sam
small_test_R2_unsorted.sam
DpnII_10k.bed
value