Repository revision
21:ea19190ce5e0

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

hicCorrectMatrix tool metadata
Miscellaneous
hicCorrectMatrix
run a Hi-C matrix correction algorithm
hicexplorer_hiccorrectmatrix
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/3.7.2+galaxy0
3.7.2+galaxy0
hicCorrectMatrix --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/3.7.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/3.6+galaxy1
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/3.6+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/3.4.3.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/3.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/3.4.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/3.3.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.4.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.0.1
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/1.8.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/1.8.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/1.7.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/hicexplorer_hiccorrectmatrix/hicexplorer_hiccorrectmatrix/1.7.1.0
hicexplorer_hiccorrectmatrix
Requirements (dependencies defined in the <requirements> tag set)
name version type
hicexplorer 3.7.2 package
Additional information about this tool
cp '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&

        hicCorrectMatrix
            $mode.mode_selector
            --matrix 'matrix.$matrix_h5_cooler.ext'

            ## special: --chromosomes is optional, but if given needs at least one argument
            #set chroms = ' '.join([ '\'' + str($var.chromosome) + '\'' for $var in $chromosomes ])
            #if chroms
                --chromosomes $chroms
            #end if

            #if $mode.mode_selector == 'correct':
                #if $mode.correctionMethod.correctionMethod_selector == 'ice':
                    --correctionMethod ICE
                    --iterNum $mode.correctionMethod.iterNum


                    #if $mode.correctionMethod.filterThreshold_low and $mode.correctionMethod.filterThreshold_large:
                        --filterThreshold $mode.correctionMethod.filterThreshold_low $mode.correctionMethod.filterThreshold_large
                    #end if

                    #if $mode.correctionMethod.inflationCutoff:
                        --inflationCutoff $mode.correctionMethod.inflationCutoff
                    #end if

                    #if $mode.correctionMethod.transCutoff:
                        --transCutoff $mode.correctionMethod.transCutoff
                    #end if

                    #if $mode.correctionMethod.sequencedCountCutoff:
                        --sequencedCountCutoff $mode.correctionMethod.sequencedCountCutoff
                    #end if

                    $mode.correctionMethod.skipDiagonal
                    $mode.correctionMethod.perchr
                #else:
                    --correctionMethod KR
                #end if
                --outFileName matrix.$matrix_h5_cooler.ext
            #elif $mode.mode_selector == 'diagnostic_plot':
                --plotName diagnostic_plot.png
                ##--outMatrixFile corrected_matrix.npz.h5
                #if $mode.xMax:
                    --xMax $mode.xMax
                #end if
                $mode.perchr
            #end if
        #if $mode.mode_selector == 'correct':
            && mv matrix.$matrix_h5_cooler.ext '$outFileName'
        #end if
None
False
Functional tests
name inputs outputs required files
Test-1 matrix_h5_cooler: small_test_matrix.h5
mode|correctionMethod|filterThreshold_low: -2.0
mode|correctionMethod|filterThreshold_large: 4
mode|correctionMethod|correctionMethod_selector: ice
mode|mode_selector: correct
chromosomes_0|chromosome: chrUextra
chromosomes_1|chromosome: chr3LHet
 name: value
 small_test_matrix.h5
value
Test-2 matrix_h5_cooler: small_test_matrix.h5
mode|correctionMethod|correctionMethod_selector: kr
mode|mode_selector: correct
 name: value
 small_test_matrix.h5
value
Test-3 matrix_h5_cooler: small_test_matrix.cool
mode|correctionMethod|correctionMethod_selector: kr
mode|mode_selector: correct
 name: value
 small_test_matrix.cool
value
Test-4 matrix_h5_cooler: small_test_matrix.h5
mode|correctionMethod|filterThreshold_low: -2.0
mode|correctionMethod|filterThreshold_large: 4
mode|correctionMethod|correctionMethod_selector: ice
mode|mode_selector: correct
chromosomes_0|chromosome: chrUextra
chromosomes_1|chromosome: chr3LHet
 name: value
 small_test_matrix.h5
value
Test-5 matrix_h5_cooler: small_test_matrix.h5
mode|mode_selector: diagnostic_plot
chromosomes_0|chromosome: chrUextra
chromosomes_1|chromosome: chr3LHet
 name: value
 small_test_matrix.h5
value