<?xml version="1.0"?>
<tool id="export" name="Retrieve Data" version="@WRAPPER_VERSION@">
  <description>from Apollo into Galaxy</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <code file="webapollo.py"/>
  <command detect_errors="aggressive"><![CDATA[
@AUTH@
python '$__tool_directory__/export.py'

@ORG_CN_OR_GUESS@

--gff '$gff_out'
$gff_with_fasta
--fasta_pep '$fasta_pep'
--fasta_cds '$fasta_cds'
--fasta_cdna '$fasta_cdna'
--vcf '$vcf_out'
--json '$json_out'
$die

'$__user_email__'

]]></command>
  <inputs>
    <expand macro="cn_or_guess" />
    <param name="gff_with_fasta" type="boolean" truevalue="--gff_with_fasta" falsevalue="" label="Include fasta in the GFF3 file" help="The fasta is available separately in the cDNA sequence file, but some tools might prefer it included in the GFF3 file."/>
    <param name="die" type="boolean" truevalue="--die" falsevalue="" label="Fail hard if any portion of the export fails" help="By default it will just print a warning message, this causes any error to be fatal."/>
  </inputs>
  <outputs>
    <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
    <data format="fasta" name="fasta_pep" label="Peptide sequences from Apollo"/>
    <data format="fasta" name="fasta_cds" label="CDS sequences from Apollo"/>
    <data format="fasta" name="fasta_cdna" label="cDNA sequences from Apollo"/>
    <data format="vcf" name="vcf_out" label="Sequence alterations from Apollo"/>
    <data format="json" name="json_out" label="Metadata from Apollo">
        <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
    </data>
  </outputs>
  <tests>
      <test>
          <conditional name="org_source">
              <param name="source_select" value="direct"/>
              <param name="org_raw" value="test_organism" />
          </conditional>
          <conditional name="cn_source">
              <param name="source_select" value="all"/>
          </conditional>

          <output name="gff_out">
              <assert_contents>
                  <has_text text="##sequence-region Merlin 1 172788" />
                  <has_text text="owner=admin@local.host;" />
              </assert_contents>
          </output>
          <output name="fasta_pep" file="export/pep.fa" lines_diff="12"/>
          <output name="fasta_cds" file="export/cds.fa" lines_diff="12"/>
          <output name="fasta_cdna" file="export/cdna.fa" lines_diff="12"/>
          <output name="vcf_out" file="export/out.vcf" lines_diff="4"/>
          <output name="json_out">
              <assert_contents>
                  <has_text text="test_organism" />
              </assert_contents>
          </output>
      </test>
  </tests>
  <help><![CDATA[
**What it does**

Exports the sequence data and annotations from Apollo.

If you provide an Apollo JSON file as input to the Organism Common Name list,
this will enable extracting multiple organism's data at once from Apollo.
Beware that currently all gff3 and fasta responses are merged together. If you
have two separate organisms with identically named reference sequences, it will
not be possible to separate those out.

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