<tool id="ceas" name="CEAS" version="1.0.2-1">
  <requirements>
    <requirement type="package" version="1.2.5">python_mysqldb</requirement>
    <requirement type="package" version="0.7.1">bx_python</requirement>
    <requirement type="package" version="1.0.2.d8c0751">cistrome_ceas</requirement>
    <requirement type="package" version="3.1.2">R</requirement>
  </requirements>
  <description>Annotate intervals and scores with genome features</description>
  <command interpreter="bash">ceas_wrapper.sh $bed_file $gdb_file $extra_bed_file $log_output $pdf_report $xls_output
  #if (str($wig_file.ext) == 'bigwig')
    --bigwig $wig_file
    --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len
  # else
    --wig $wig_file
  #end if
  #if (str($span) and int(str($span)) > 0)
    --span $span
  #end if
  --sizes $sizes_lower,$sizes_middle,$sizes_upper
  --bisizes $bisizes_lower,$bisizes_upper
  --pf-res $profiling_resolution
  --rel-dist $relative_distance</command>
  <inputs>
    <param name="bed_file" type="data" format="bed" label="BED file with ChIP regions" />
    <param name="wig_file" type="data" format="wig,bigwig" label="WIG or BIGWIG file for wig profiling or genome background annotation" optional="true" />
    <param name="extra_bed_file" type="data" format="bed" label="BED file with extra regions of interest (e.g. non-coding regions)" optional="true" />
    <param name="gdb_file" type="select" label="Gene annotation table">
      <options from_data_table="ceas_annotations">
	<filter name="dbkey" type="data_meta" ref="bed_file" key="dbkey" column="0" />
        <validator type="no_options" message="No tables are available for the selected input"/>
      </options>
    </param>
    <param name="span" type="integer" label="Span from TSS and TTS in the gene-centered annotation (bp)" help="ChIP regions within this range from TSS and TTS are considered when calculating the coverage rates of promoter and downstream by ChIP regions" value="3000" />
    <param name="sizes_lower" type="integer" label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)" value="1000" />
    <param name="sizes_middle" type="integer" label="Middle interval for promoter/downstream sizes (bp)" value="2000" help="Values > 10000bp are automatically fixed to 10000bp" />
    <param name="sizes_upper" type="integer" label="Upper interval for promoter/downstream sizes (bp)" value="3000" help="Values > 10000bp are automatically fixed to 10000bp" />
    <param name="bisizes_lower" type="integer" label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500" />
    <param name="bisizes_upper" type="integer" label="Upper interval for bidirectional-promoter sizes (bp)" value="5000" help="Values > 20000bp are automatically fixed to 20000bp" />
    <param name="profiling_resolution" type="integer" label="Wig profiling resolution (bp)" value="50" help="Warning: a number smaller than the wig interval (resolution) may cause aliasing error" />
    <param name="relative_distance" type="integer" label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000" />
  </inputs>
  <outputs>
    <data name="log_output" format="txt" label="CEAS on ${on_string} (log output)" />
    <data name="pdf_report" format="pdf" label="CEAS on ${on_string} (PDF report)" />
    <data name="xls_output" format="interval" label="CEAS on ${on_string} (XLS output)" />
  </outputs>
  <help>
**What it does**

CEAS (Cis-regulatory Element Annotation System) is a tool for characterizing genome-wide
protein-DNA interaction patterns from ChIP-chip and ChIP-Seq of both sharp and broad
binding factors. It provides statistics on ChIP enrichment at important genome features
such as specific chromosome, promoters, gene bodies, or exons, and infers genes most
likely to be regulated by a binding factor.

CEAS also enables biologists to visualize the average ChIP enrichment signals over
specific genomic features, allowing continuous and broad ChIP enrichment to be perceived
which might be too subtle to detect from ChIP peaks alone.

This tool is compatible with the ceasBW version of CEAS from the Cistrome package
obtained from

https://bitbucket.org/cistrome/cistrome-applications-harvard/overview

(commit id d8c0751, datestamp 20140929). The CEAS code is under the
published-packages/CEAS/ subdirectory.

Cistrome data files and documentation can be found at

http://liulab.dfci.harvard.edu/CEAS/index.html

The CEAS user manual is available at http://liulab.dfci.harvard.edu/CEAS/usermanual.html
  </help>
</tool>