view gff3_require_phage_start.xml @ 0:10c9beb60fbc draft default tip

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<tool id="edu.tamu.cpt.gff3.require_phage_start" name="GFF3 Filter: Require Phage Start" version="19.1.0.0">
  <description>ensures start is ATG, TTG, or GTG</description>
  <macros>
    <import>macros.xml</import>
		<import>cpt-macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
@GENOME_SELECTOR_PRE@

python $__tool_directory__/gff3_require_phage_start.py

@GENOME_SELECTOR@
$gff3_data

> $stdout

]]></command>
  <inputs>
    <expand macro="genome_selector" />
    <expand macro="gff3_input" />
  </inputs>
  <outputs>
    <data format="gff3" name="stdout" label="$gff3_data.name filtered for start codon"/>
  </outputs>
  <tests>
      <test>
			<param name="reference_genome_source" value="history" />
			<param name="genome_fasta" value="T7_ReqPhageIn.fasta" />
			<param name="gff3_data" value="T7_ReqPhageIn.gff3" />

          <output name="stdout" file="T7_ReqPhageOut.gff3" />
      </test>
      <test>
			<param name="reference_genome_source" value="history" />
			<param name="genome_fasta" value="Miro_ReqPhageIn.fa" />
			<param name="gff3_data" value="Miro_ReqPhageIn.gff3" />

          <output name="stdout" file="Miro_ReqPhageOut.gff3" />
      </test>
  </tests>
  <help><![CDATA[
**What it does**

Removes any CDS from the GFF3 whose start codon is **not** ATG, TTG, or GTG.

.. class:: warningmark

The tool only retains *gene* and *CDS* features that pass this filter. 
      ]]></help>
		<expand macro="citations" />
</tool>