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ChIPseeker tool metadata

Miscellaneous

Name: ChIPseeker

Description: for ChIP peak annotation and visualization

Id: chipseeker

Guid: toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.28.3+galaxy0

Version: 1.28.3+galaxy0

Version command string: echo $(R --version | grep version | grep -v GNU)", ChIPseeker version" $(R --vanilla --slave -e "library(ChIPseeker); cat(sessionInfo()\$otherPkgs\$ChIPseeker\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", optparse version" $(R --vanilla --slave -e "library(optparse); cat(sessionInfo()\$otherPkgs\$optparse\$Version)" 2> /dev/null | grep -v -i "WARNING: ")

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.28.3+galaxy0 (this tool)

toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.18.0+galaxy1

toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.18.0

toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.16.2

toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.16.1

toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.14.2.2

toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.14.2.1

toolshed.g2.bx.psu.edu/repos/rnateam/chipseeker/chipseeker/1.14.2

chipseeker

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

bioconductor-chipseeker

1.28.3

package

r-optparse

1.6.6

package

Additional information about this tool

Command:

#set gtf = "refgtf"
        #if $gtf_source.gtf_source_select == "history":
            ln -s '${gtf_source.gtf_hist}' $gtf &&
        #else if $gtf_source.gtf_source_select == "cached":
            ln -s '${gtf_source.gtf_builtin.fields.path}' $gtf &&
        #end if

        #if $rscript:
            cp '$__tool_directory__/chipseeker.R' '$out_rscript' &&
        #end if

        Rscript '$__tool_directory__/chipseeker.R'

        -i '$peaks'
        -H $header
        -G '$gtf'
        -u $adv.upstream
        -d $adv.downstream

        #if $adv.flankgeneinfo:
            -F $adv.flankgeneinfo
        #end if

        -D $adv.flankgenedist

        #if $adv.ignoreUpstream:
            -j $adv.ignoreUpstream
        #end if

        #if $adv.ignoreDownstream:
            -k $adv.ignoreDownstream
        #end if

        -f $format

        #if $pdf:
            -p $pdf
        #end if

        -r $rdata

Interpreter: None

Forces a history refresh: False

Functional tests

name

inputs

outputs

required files

Test-1

peaks: in.bed
gtf_source|gtf_hist: in.gtf
gtf_source|gtf_source_select: history
rscript: True
rdata: True

name: value
name: value
name: value
name: value

in.bed
in.gtf
value

Test-2

peaks: in.interval
gtf_source|gtf_source_select: cached

name: value
name: value

in.interval
value

Test-3

peaks: in.interval
gtf_source|gtf_hist: in.gtf
gtf_source|gtf_source_select: history
format: tabular

name: value
name: value

in.interval
in.gtf
value

Test-4

peaks: in.interval
gtf_source|gtf_hist: in.gtf
gtf_source|gtf_source_select: history
format: tabular
adv|upstream: 1000
adv|downstream: 1000

name: value
name: value

in.interval
in.gtf
value

Test-5

peaks: in.interval
gtf_source|gtf_hist: in.gtf
gtf_source|gtf_source_select: history
format: tabular
adv|flankgeneinfo: True

name: value
name: value

in.interval
in.gtf
value

Test-6

peaks: in.interval
gtf_source|gtf_source_select: cached
pdf: False

name: value

in.interval
value