view gff3_extract_sequence2.xml @ 3:5e8787e39d30 draft default tip

planemo upload commit f33bdf952d796c5d7a240b132af3c4cbd102decc

<tool id="edu.tamu.cpt.gff3.export_seq_unique" name="Feature Sequence Export Unique" version="1.2">
  <description>specially modified for sending CDSs to blast</description>
  <macros>
    <import>macros.xml</import>

  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
@GENOME_SELECTOR_PRE@

'$__tool_directory__/gff3_extract_sequence.py'
@GENOME_SELECTOR@

@INPUT_GFF@

--feature_filter unique_cds
'$nodesc'
> '$default'
2> '$gff3'
]]></command>
  <inputs>
    <expand macro="genome_selector"/>
    <expand macro="gff3_input"/>
    <param label="Remove description (use if blasting)" name="nodesc" type="boolean" truevalue="--nodesc" falsevalue=""/>
  </inputs>
  <outputs>
    <data format="fasta" hidden="false" name="default"/>
    <data format="gff3" hidden="false" name="gff3"/>
  </outputs>
  <help><![CDATA[
**What it does**

Extract fasta sequences from a parent genome.
      ]]></help>
  <expand macro="citations"/>
</tool>