<tool name="Extract data from Bed" id="bed_for_chrom">
  <description>Extract data for certain chromosome from a BED file</description>
  <command interpreter="command">/bin/bash $shscript</command>
  <inputs>
    <param ftype="bed" format="bed" name="bfile" type="data" label="BED file"/>
    <param name="chrom" type="text" label="Chromosome" optional="false" />
  </inputs>
  <outputs>
    <data format="bed" name="output" />
  </outputs>
  <configfiles>
    <configfile name="shscript">
#!/bin/bash

#set $dollar = chr(36)
#set $gt = chr(62)
#set $lt = chr(60)
#set $ad = chr(38)
#set $up = chr(94)

chromlength=`echo $chrom |awk '{print length(${dollar}0)}'`
if [[ ${dollar}chromlength -gt 255 ]];then
    echo "Chromosome exceed the limit of 255 characters!" ${gt}${ad}2;
    exit;
fi
if [[ ${dollar}chromlength -eq 0 ]];then
    echo "Chromosome is required!" ${gt}${ad}2;
    exit;
fi

grep -w ${up}${chrom} $bfile ${ad}${gt} $output

     </configfile>
  </configfiles>
<tests>
  <test maxseconds="3600" name="BedExtract_1">
    <param name="bfile" value="bedfile.bed" />
    <param name="chrom" value="chrX" />
    <output name="output" file="bedextract_1/bedextract_1.bed" />
  </test>
  <test maxseconds="3600" name="BedExtract_2">
    <param name="bfile" value="bedfile.bed" />
    <param name="chrom" value="chr1" />
    <output name="output" file="bedextract_2/bedextract_2.bed" />
  </test>
</tests>
  <help>
This tool can extract the scores for a certain chromosome with a big
BED file.

-----

**Parameters**

- **BED file** is selected from history. 
- **Chromosome** on which the regions will be extracted from the BED
  file.

-----

**Output**

- **BED file** only contains the scores for a certain chromosome.

  </help>

</tool>