view gene_fraction.xml @ 0:0fd352f62446 draft default tip

planemo upload for repository https://github.com/ChrisD11/Duplicon commit 3ee0594c692faac542ffa58f4339d79b9b8aefbd-dirty

<tool id="gene_fraction" name="Gene Fraction" version="0.1.0">
  <description>for single-end or paired-end data</description>
  <command>$__tool_directory__/csa -amr_fp $amr_fp -sam_fp $sam_fp -t $threshold -min $min -max $max -skip $skip -samples $samples -out_fp $out_fp</command>
  <inputs>
    <param format="fasta" name="amr_fp" type="data" label="Input fasta file"/>
    <param format="sam" name ="sam_fp" type="data" label="Input SAM file"/>
    <param name="threshold" size="3" type="integer" min="0" max="100" value="1" label="Threshold"/>
    <param name="min" size="3" type="integer" min="1" max="100" value="1" label="Minimum level"/>
    <param name="max" size="3" type="integer" min="1" max="100" value="1" label="Maximum level"/>
    <param name="skip" size="3" type="integer" min="1" max="100" value="1" label="Skip pattern"/>
    <param name="samples" size="3" type="integer" min="1" max="100" value="1" label="Samples per level"/>
  </inputs>
  <outputs>
    <data format="tabular" name="out_fp" />
  </outputs>
  <help>
This tool calculates the amount of genes that are covered by atleast one read.
  </help>

</tool>