<tool id="wellington_footprints" name="Wellington Footprints" version="0.2.5">
  <description>accurate identification of digital genomic footprints from DNase-seq data</description>
  <requirements>
    <requirement type="package">pymodules</requirement>
  </requirements>
  <command>
#set $final_output = $output.extra_files_path + "/input.bam.input.bed.WellingtonFootprints.FDR.0.01.bed"
mkdir $output.extra_files_path;
ln -s $bam_file input.bam;
ln -s $bam_file.metadata.bam_index input.bam.bai;
ln -s $bed_file input.bed;
wellington_footprints.py input.bed input.bam $output.extra_files_path -fdrlimit $fdrlimit;
cp $final_output $output;
rm -rf $output.extra_files_path
  </command>
  <stdio>
    <exit_code range="1:" level="fatal" description="Error produced" />
  </stdio>
  <inputs>
    <param help="" format="bam" label="Input BAM" name="bam_file" type="data"/>
    <param help="" format="bed" label="Input BED" name="bed_file" type="data"/>
    <param help="" label="FDR Limit" value="0"  name="fdrlimit" type="integer"/>
  </inputs>

   <outputs>
         <data format="bed" label="${tool.name} on ${on_string}" name="output" />
   </outputs>
   <tests>
     <test>
     </test>
   </tests>
   <help>
   </help>
</tool>