Repository revision
19:7ef978dc1b8a

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

computeMatrixOperations tool metadata
Miscellaneous
Modify or combine the output of computeMatrix in a variety of ways.
deeptools_compute_matrix_operations
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.5.2+galaxy0
3.5.2+galaxy0
computeMatrixOperations --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.5.4+galaxy0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.5.2+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.3.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.2.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.2.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.1.2.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.0.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.0.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/3.0.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/2.5.7.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/2.5.1.1.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/2.5.1.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/2.5.0.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/2.4.2.0
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools_compute_matrix_operations/deeptools_compute_matrix_operations/2.4.1.0
deeptools_compute_matrix_operations
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
computeMatrixOperations
            #if $submodule.command == "info":
                info
                -m $submodule.matrixFile
                > $outFileTxt
            #else if $submodule.command == "relabel":
                relabel
                -m $submodule.matrixFile
                #if $submodule.groupLabels is not None and str($submodule.groupLabels) != '':
                    --groupLabels $submodule.groupLabels
                #end if
                #if $submodule.sampleLabels is not None and str($submodule.sampleLabels) != '':
                    --sampleLabels $submodule.sampleLabels
                #end if
            #else if $submodule.command == "subset":
                subset
                -m $submodule.matrixFile
                #if $submodule.groups is not None and str($submodule.groups) != '':
                    --groups $submodule.groups
                #end if
                #if $submodule.samples is not None and str($submodule.samples) != '':
                    --samples $submodule.samples
                #end if
                -o $outFileName
            #else if $submodule.command == "filterStrand":
                filterStrand
                -m $submodule.matrixFile
                --strand $submodule.strand
                -o $outFileName
            #else if $submodule.command == "filterValues":
                filterValues
                -m $submodule.matrixFile
                #if $submodule.minValue is not None and str($submodule.minValue) != '':
                    --min $submodule.minValue
                #end if
                #if $submodule.maxValue is not None and str($submodule.maxValue) != '':
                    --max $submodule.maxValue
                #end if
                -o $outFileName
            #else if $submodule.command == "rbind":
                #set $files=[]
                #for $f in $submodule.matrixFiles:
                    #silent $files.append(str($f.matrixFile))
                #end for
                rbind
                -m '#echo "' '".join($files)#'
                -o $outFileName
            #else if $submodule.command == "cbind":
                cbind
                #set $files=[]
                #for $f in $submodule.matrixFiles:
                    #silent $files.append(str($f.matrixFile))
                #end for
                -m '#echo "' '".join($files)#'
                -o $outFileName
            #else if $submodule.command == "sort":
                sort
                #set $files=[]
                #for $f in $submodule.regionsFiles:
                    #silent $files.append(str($f.regionsFile))
                #end for
                -m $submodule.matrixFile
                -R '#echo "' '".join($files)#'
                -o $outFileName
            #else if $submodule.command == "dataRange":
                dataRange
                -m $submodule.matrixFile
                > $outFileTxt
            #end if

    
None
False
Functional tests
name inputs outputs required files
Test-1 submodule|matrixFile: computeMatrix_result1.gz
submodule|command: info
name: value
computeMatrix_result1.gz
value
Test-2 submodule|matrixFiles_0|matrixFile: computeMatrix_result1.gz
submodule|matrixFiles_1|matrixFile: computeMatrix_result1.gz
submodule|command: rbind
name: value
computeMatrix_result1.gz
value