view build_ceasdb.xml @ 3:f404ec7f679c

Add Conservation Plot tool

<tool name="CEAS: build database" id="ceas_build_db" version="0.1.0">
  <description>with gene annotation and genome background</description>
  <macros>
    <import>ceas_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command interpreter="command">
  build_genomeBG 
  #if $ref.refsrc == 'ucsc':
  -d $ref.dbkey -g $ref.gene_table
  #elif $ref.refsrc == 'history':
  -g $ref.gdb
  #elif $ref.refsrc == 'cached':
  -g $ref.ceas_db
  #end if
  -w $wfile -o $output
  </command>
  <inputs>
    <conditional name="ref">
      <param name="refsrc" type="select" label="">
        <option value="ucsc">From UCSC</option>
        <option value="history">From history</option>
        <option value="cached">Locally cached CEAS db</option>
      </param>
      <when value="ucsc">
        <param name="dbkey" type="text" value="" label="A UCSC genome id, e.g. mm9">
        </param>
        <param name="gene_table" type="text" value="" label="A UCSC gene table name, e.g. refGene">
        </param>
      </when>
      <when value="cached">
        <param name="ceas_db" type="select" label="">
          <options from_data_table="ceasdb">
            <filter type="unique_value" column="0" />
          </options>
        </param>
      </when>
      <when value="history">
        <param name="gdb" type="data" format="ceasdb" label="Gene annotation table file (sqlite3)">
        </param>
      </when>
    </conditional>
    <param name="wfile" type="data" format="wig,bigwig"  label="wig / bigwig file">
      <!-- <validator type="unspecified_build" /> -->
    </param>
  </inputs>
  <outputs>
   <data format="ceasdb" name="output" label=""/>
  </outputs>
 <tests>
</tests> 
  <help>
** CEAS **
This tool annotates the given intervals and scores with genome
features such as gene body. It's the major module in CEAS package
which is written by Hyunjin Gene Shin, published in Bioinformatics
(pubmed id:19689956).

@EXTERNAL_DOCUMENTATION@

@CITATION_SECTION@

  </help>

</tool>