annotate ceas_wrapper.xml @ 3:df54f8fcc7a7 draft

Version 1.0.2-3: move to conda-based dependency resolution.

<tool id="ceas" name="CEAS" version="1.0.2-3">
  <description>Annotate intervals and scores with genome features</description>
  <requirements>
    <requirement type="package" version="1.0.2b1">cistrome-ceas</requirement>
    <requirement type="package" version="357">ucsc-fetchchromsizes</requirement>
  </requirements>
  <version_command>ceas --version 2&gt;&amp;1 | tail -1</version_command>
  <command><![CDATA[
  bash $__tool_directory__/ceas_wrapper.sh
  $bed_file ${gdb_file.fields.path}
  $log_output $pdf_report $xls_output
  #if (str($wig_file) != 'None')
    #if (str($wig_file.ext) == 'bigwig')
      --bigwig $wig_file
      --length $GALAXY_DATA_INDEX_DIR/shared/ucsc/chrom/${bed_file.dbkey}.len
    #else
      --wig $wig_file
    #end if
  #end if
  #if (str($extra_bed_file) != 'None')
    --ebed $extra_bed_file
  #end if
  #if (str($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"
	   help="If not supplied then only perform ChIP region annotation and gene-centered annotation" />
    <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">
      </options>
      <filter name="dbkey" type="data_meta" ref="bed_file" key="dbkey" column="1" />
      <validator type="no_options" message="No tables are available for the selected input"/>
    </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 (--span)" value="3000" />
    <param name="sizes_lower" type="integer"
	   label="Lower interval for promoter/downstream sizes for ChIP region annotation (bp)"
	   value="1000" help=" (--sizes)" />
    <param name="sizes_middle" type="integer"
	   label="Middle interval for promoter/downstream sizes (bp)" value="2000"
	   help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
    <param name="sizes_upper" type="integer"
	   label="Upper interval for promoter/downstream sizes (bp)" value="3000"
	   help="Values > 10000bp are automatically fixed to 10000bp (--sizes)" />
    <param name="bisizes_lower" type="integer"
	   label="Lower interval for bidirectional-promoter sizes for ChIP region annotation (bp)" value="2500"
	   help="(--bisizes)" />
    <param name="bisizes_upper" type="integer"
	   label="Upper interval for bidirectional-promoter sizes (bp)" value="5000"
	   help="Values > 20000bp are automatically fixed to 20000bp (--bisizes)" />
    <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 (--pf-res)" />
    <param name="relative_distance" type="integer"
	   label="Relative distance to TSS/TTS in wig profiling (bp)" value="3000"
	   help="(--rel-dist)" />
  </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>
  <tests>
    <test>
      <!-- Test with bed input only -->
      <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
      <param name="gdb_file" value="galGal3_test" />
      <output name="log_output" file="ceas_out1.log.re_match" compare="re_match"/>
      <output name="pdf_report" file="ceas_out1.pdf" />
      <output name="xls_output" file="ceas_out1.xls" />
    </test>
    <test>
      <!-- Test with bed & very small wig input -->
      <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
      <param name="wig_file" value="ceas_in.wig" ftype="wig" />
      <param name="gdb_file" value="galGal3_test" />
      <output name="log_output" file="ceas_out2.log.re_match" compare="re_match"/>
      <output name="pdf_report" file="ceas_out2.pdf" />
      <output name="xls_output" file="ceas_out2.xls" />
    </test>
    <test>
      <!-- Test with bed & bigwig input -->
      <param name="bed_file" value="ceas_in.bed" ftype="bed" dbkey="galGal3" />
      <param name="wig_file" value="ceas_in.bigwig" ftype="bigwig" />
      <param name="gdb_file" value="galGal3_test" />
      <output name="log_output" file="ceas_out3.log.re_match" compare="re_match"/>
      <output name="pdf_report" file="ceas_out3.pdf" />
      <output name="xls_output" file="ceas_out3.xls" />
    </test>
  </tests>
  <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.

**Usage**

CEAS takes the following inputs:

 * BED file with discrete ChIP regions (for example, the 'summits' output from the MACS
   peak caller)
 * WIG or bigWIG file with a continuous ChIP enrichment signal
 * Gene annotation table (provided as reference data)

Optionally it can also take a BED file describing extra regions of interest (for example
non-coding regions).

The analysis modules are:

 * **ChIP region annotation:** estimates the relative enrichment level of ChIP regions in
   each gene feature with respect to the whole genome.
 * **Gene-centered annotation:** identifies genes associated with ChIP regions to infer
   the direct regulatory gene targets of the binding factor of interest.
 * **Average signal profiling within/near important genomic features:** displays continuous
   ChIP enrichment signal within/around important gene features to help visualize the
   average binding patterns.

**Background**

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>
  <citations>
    <!--
    See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
    Can be either DOI or Bibtex
    Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
    -->
    <citation type="doi">10.1093/bioinformatics/btp479</citation>
  </citations>
</tool>