<?xml version="1.0"?>
<tool id="feat_from_gff3" name="GFF3 to Apollo Annotations" version="@WRAPPER_VERSION@">
  <description></description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <code file="webapollo.py"/>
  <command detect_errors="aggressive"><![CDATA[
@AUTH@

python '$__tool_directory__/create_features_from_gff3.py'
@ORG_OR_GUESS@

'$__user_email__'
'$gff3_data'
--source '${__app__.config.galaxy_infrastructure_url}/history/view/${__app__.security.encode_id($gff3_data.history_id)}'
$use_name
$disable_cds_recalculation

> '$output']]></command>
  <inputs>
    <expand macro="org_or_guess" />
    <expand macro="gff3_input" />
    <param name="use_name" type="boolean" truevalue="--user_name" falsevalue="" label="Use the given name instead of generating one" />
    <param name="disable_cds_recalculation" type="boolean" truevalue="--disable_cds_recalculation" falsevalue="" label="Disable CDS recalculation and instead use the one provided" />
  </inputs>
  <outputs>
    <data format="txt" name="output" label="Process and Error Log"/>
  </outputs>
  <tests>
      <test>
          <conditional name="org_source">
              <param name="source_select" value="direct"/>
              <param name="org_raw" value="Test org" />
          </conditional>
          <param name="gff3_data" value="merlin.gff"/>
          <output name="output" file="load_gff3/output.txt" compare="sim_size"/>
      </test>
  </tests>
  <help><![CDATA[
@REFERENCES@
]]></help>
  <expand macro="citations"/>
</tool>