view export.xml @ 7:db216690cbbf draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit b9143221aee2cd09e1334ee56ff9651550b1797a
author gga
date Fri, 15 Mar 2019 06:03:48 -0400
parents 950fb2bf116d
children f45ad96c9e08
line wrap: on
line source

<?xml version="1.0"?>
<tool id="export" name="Retrieve Data" version="3.1">
  <description>from Apollo into Galaxy</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <code file="webapollo.py"/>
  <command detect_errors="aggressive"><![CDATA[
python $__tool_directory__/export.py

@ADMIN_AUTH@

@ORG_CN_OR_GUESS@

--gff "$gff_out"
--fasta "$fasta_out"
--json "$json_out"

"$__user_email__"

]]></command>
  <inputs>
    <expand macro="cn_or_guess" />
  </inputs>
  <outputs>
    <data format="gff3" name="gff_out" label="Annotations from Apollo"/>
    <data format="fasta" name="fasta_out" label="Sequence(s) 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 expect_failure="true">
          <conditional name="org_source">
              <param name="source_select" value="direct"/>
              <param name="org_raw" value="Test org" />
          </conditional>
          <conditional name="cn_source">
              <param name="source_select" value="all"/>
          </conditional>
          <expand macro="test_result" />
      </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>