Revision: 34:c3ef5377a571

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/alenail/chipsequtil

Miscellaneous

Name: Map Peaks to Known Genes

Description: Map the peaks in <peaks file> to genes in <knownGene file>. <knownGene file> isformat is as specified in http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/knownGene.sql.<peaks file> format is as produced by MACS. If *auto* is chosen (default) file extension is examined for *.xls* for default MACS format or *.bed* for BED format. If the --detail option is provided, the following extra fields are appended to each row: peak loc, dist from feature, map type, map subtype

Id: chipsequtil_maptoknowngenes

Guid: toolshed.g2.bx.psu.edu/repos/alenail/chipsequtil/chipsequtil_maptoknowngenes/0.1

Version: 0.1

Version command string: None

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/alenail/chipsequtil/chipsequtil_maptoknowngenes/0.1 (this tool)

chipsequtil_maptoknowngenes

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

Requirements:

name	version	type
chipsequtil	1.0	package

Additional information about this tool

Command:

map_to_known_genes.py
      $tss
      --peaks-format=$peaks_fmt
      --upstream-window=$upst_win
      --downstream-window=$dnst_win
      --map-output="$peaksOutput"
      $detail
      $intergenic
      $knownGeneFile $knownGeneRef $macsPeaksFile

  

Interpreter: python

Forces a history refresh: False

Parallelism

Method: basic

split_size: 20

split_mode: number_of_parts

Functional tests

No functional tests defined