<?xml version="1.0"?>
<tool id="feat_from_gff3" name="GFF3 to Apollo Annotations" version="1.0">
  <description></description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <code file="webapollo.py"/>
  <command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/create_features_from_gff3.py
@ADMIN_AUTH@
@ORG_OR_GUESS@

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

> $output]]></command>
  <inputs>
    <expand macro="org_or_guess" />
    <expand macro="gff3_input" />
  </inputs>
  <outputs>
	<data format="tabular" name="output" label="Process and Error Log">
        <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
    </data>
  </outputs>
  <tests>
      <test expect_failure="true">
          <conditional name="org_source">
              <param name="source_select" value="direct"/>
              <param name="org_raw" value="Test org" />
          </conditional>
          <param name="gff3_data" value="good-model.gff3"/>
          <expand macro="test_result" />
      </test>
  </tests>
  <help><![CDATA[
**NOTA BENE**

This is **incredibly, highly experimental**

DO NOT:

-  Run on gff3 referencing multiple reference sequences/contigs
-  Expect it to work well
-  Expect it to work at all

@REFERENCES@
]]></help>
  <expand macro="citations"/>
</tool>