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<tool name="GCA: Gene centered annotation" id="ceas_gca" version="0.1.0">
  <description>Find the nearest interval in the given intervals set fo every annotated coding gene</description>
  <macros>
    <import>ceas_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command>
gca -b $bfile --span=$span 
#include source=$gtpath_ceasdb_ref#
--name=$name &amp;> $log
  </command>
  <inputs>
    <param name="name" type="hidden" value="gca_out"/>
    <param ftype="bed" format="bed" name="bfile" type="data" label="BED file(100,000 lines max)">
      <validator type="unspecified_build" />
    </param>
    <expand macro="ceasdb_ref" />
    <param name="span" type="text" label="Span" value="3000">
    	<validator type="in_range" max="1000000" min="100" message="Span is out of range, Span has to be between 100 to 1000000" />
    </param>
  </inputs>
  <outputs>
    <data format="xls" name="output" from_work_dir="gca_out.xls"/>
    <data format="txt" name="log" label="GCA job log"/>
  </outputs>
  <expand macro="stdio" />
  <tests>
    <test maxseconds="3600" name="GCA_1">
      <param name="bfile" value="peaks.bed" />
      <param name="span" value="3000" />
      <param name="refsrc" value="history"/>
      <param name="gdb" ftype="ceasdb" value="mm9.refGene.ceasdb"/>
      <output name="output">
        <assert_contents>
          <has_text_matching expression="NM_013495\tchr19\t3323300\t3385733\t+\t2994\t754\t31798\t224353\t0.07\t0.26\t0.12\t0.03\t0.0\t0.0\t0.0" />
        </assert_contents>
      </output>
    </test>
  </tests>
  <help>
This tool finds the nearest binding sites in the given BED file for
every annotated coding gene. It's a module in CEAS package which is
written by Hyunjin Gene Shin, published in Bioinformatics (pubmed
id:19689956).

@EXTERNAL_DOCUMENTATION@

@CITATION_SECTION@

.. class:: warningmark

**NEED IMPROVEMENT**

-----

**Parameters**

- **BED file** contains the transcription factor binding sites,
  generally the BED files for peaks from peak calling tools.
- **Span** is the span for ChIP regions.
- **Genome Annotation Version** to specify the annotations according to
  the data set. The annotations are downloaded from UCSC genome site.

-----

**Output**

- **XLS file** is the tab-delimited file.

-----

**script parameter list of GCA**

Options:
  --version            show program's version number and exit
  -h, --help           Show this help message and exit.
  -b BED, --bed=BED    BED file of ChIP regions.
  -g GDB, --gt=GDB     Gene annotation table. This can be a sqlite3 local db
                       file, BED file or genome version of UCSC. The BED file
                       must have an extension of '.bed'
  --span=SPAN          Span in search of ChIP regions from TSS and TTS,
                       DEFAULT=3000bp
  --name=NAME          Experiment name. This will be used to name the output
                       file. If an experiment name is not given, input BED
                       file name will be used instead.
  --gn-group=GN_GROUP  A particular group of genes of interest. If a txt file
                       with one column of gene names (eg RefSeq IDs in case of
                       using a refGene table) is given, gca returns the gene-
                       centered annotation of this particular gene group.
  --gname2=NAME2       The gene names of --gn-group will be regarded as
                       'name2.' See the schema of the gene annotation table.

  </help>

</tool>