view ceas_macros.xml @ 3:f404ec7f679c

Add Conservation Plot tool

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="2014-09-16">cistrome</requirement>
        </requirements>
    </xml>
    <xml name="requirements_bx">
        <requirements>
            <requirement type="package" version="2014-09-16">cistrome</requirement>
            <requirement type="package" version="0.7.1">bx-python</requirement>
        </requirements>
    </xml>
  <xml name="stdio">
    <stdio>
        <exit_code range=":-1"  level="fatal" description="Error: Cannot open file" />
        <exit_code range="1:"  level="fatal" description="Error" />
    </stdio>
  </xml>
  <xml name="ceasdb_ref">
    <conditional name="ref">
      <param name="refsrc" type="select" label="">
        <option value="cached">cached</option>
        <option value="history">history</option>
        <!--
        <option value="build">build</option>
        -->
      </param>
      <when value="cached">
        <param name="ceasdb" 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)"/>
      </when>
      <!--
      <when value="build">
      </when>
      -->
    </conditional>
  </xml>

  <template name="script_chars">
#set global $dollar = chr(36)
#set global $gt = chr(62)
#set global $lt = chr(60)
#set global $ad = chr(38)
  </template>

  <template name="gtpath_ceasdb_ref">
#if $ref.refsrc == 'history':
 -g $ref.gdb
#elif $ref.refsrc == 'cached':
 -g $ref.ceasdb.fields.path
## #elif $ref.refsrc == 'build':
## #else:
##  -g os.path.join( os.path.abspath($__app__.config.cistrome_static_library_path), "ceaslib", "GeneTable", $dbkey )
#end if
  </template>
  <template name="validate_bedfile_sh">
##check line count and file format accuracy of bed file
lines=`wc -l $bfile | tail -1 | awk '{print ${dollar}1}'`
## bypass validation for now
## format=`$path/validation/fcfunc.py $bfile`
format="passed"
if [[ ${dollar}lines -gt 100000 ]];then
  echo "BED file is too big! 100K lines are the maximum!" ${gt}${ad}2
  exit;
fi
if [[ ${dollar}format != "passed" ]]; then
  echo ${dollar}format ${gt}${ad}2
  exit;
fi
  </template>

  <token name="@EXTERNAL_DOCUMENTATION@">

For details about this application, please go to:
	http://liulab.dfci.harvard.edu/CEAS/usermanual.html

Prebuilt reference Gene annotation tables (SQLite3) are available at:
	http://liulab.dfci.harvard.edu/CEAS/download.html
	http://liulab.dfci.harvard.edu/CEAS/src/

Set the dataset datatype to: "ceasdb" when uploading to your history.

  </token>
  <token name="@CITATION_SECTION@">------

**Citation**

For the underlying tool, please cite the following publication:
"CEAS: cis-regulatory element annotation system", Hyunjin Shin, Tao Liu, Arjun K. Manrai, and X. Shirley Liu, 
Bioinformatics. 2009 Oct 1;25(19):2605-6. doi: 10.1093/bioinformatics/btp479. Epub 2009 Aug 18.

  </token>
</macros>