<tool id="filter_spades_output" name="Filter SPAdes output" version="0.1">
  <description>remove low coverage and short contigs/scaffolds</description>
  <command interpreter="perl">filter_spades_output.pl 
  --coverage-cutoff $coverage_co
  --length-cutoff $length_co
  #if $keep_leftover
    --filtered-out $filtered_out
  #end if
  --tab $stats_in
  $fasta_in > $fasta_output
  </command>
  
  <inputs>
    <param name="fasta_in" type="data" format="fasta" label="Sequences" help="Contigs or scaffolds. Make sure you input the corresponding stat file" />
    <param name="stats_in" type="data" format="tabular" label="Contig stats" />
    <param name="length_co" type="integer" value="1000" min="0" label="Length cut-off" help="Contigs with length under that value are shown in red" />
    <param name="coverage_co" type="integer" value="10" min="0" label="Coverage cut-off" help="Contigs with length under that value are shown in red" />
    <param name="keep_leftover" type="boolean" checked="false" label="Save filtered-out sequences?" />
  </inputs>
  <outputs>
    <data format="fasta" name="fasta_output" label="Filtered sequences" />
    <data format="fasta" name="filtered_out" label="Discarded sequences"> 
      <filter>keep_leftover == "true"</filter>
    </data>
  </outputs>
  <help>
**What it does**

Using the output of SPAdes (a fasta and a stats file, either from contigs or scaffolds), it filters the fasta files, discarding all sequences that are under a given length or under a given coverage.

Typically, this is used to discard short contigs, or contaminations. To display a coverage vs. length plot, use the "SPAdes stats" tool in the same package.
  </help>
</tool>