<tool id="sm_dos2unix" name="Clean Windows files">
  <description>in order to be used on cluster (unix)</description>
  <command interpreter="perl">sm_dos2unix.pl 
  $input
  $output
  </command>
  <inputs>
    <param format="fastq, fasta, txt, bam, sam, Csfasta, qual, bed, csv, xls, gff, gtf, pdf, vcf, xsq, bw, png, tabular" name="input" type="data" label="Input file"/>
  </inputs>
  <outputs>
    <data format="fastq, fasta, txt, bam, sam, Csfasta, qual, bed, csv, xls, gff, gtf, pdf, vcf, xsq, bw, png, tabular" name="output" label="{$input.name}-cleaned" />
  </outputs>
  <help>
This command (dos2unix) cleans files from Windows in order to be used with unix.
  </help>
</tool>