annotate list_organisms.xml @ 14:a31493bc7952 draft

"planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit 7f274d9deece87f6837ffb0a22d9231671be4542"

<?xml version="1.0"?>
<tool id="list_organism" name="List Organisms" version="@WRAPPER_VERSION@">
  <description>in Apollo</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <expand macro="requirements"/>
  <command detect_errors="aggressive"><![CDATA[
@AUTH@

python '$__tool_directory__/list_organisms.py'
'$__user_email__'
> '$output']]></command>
  <inputs>
  </inputs>
  <outputs>
    <data format="json" name="output">
        <discover_datasets pattern="(?P&lt;designation&gt;.+)\.txt" format="tabular" visible="true"/>
    </data>
  </outputs>
  <tests>
      <test>
        <output name="output">
            <assert_contents>
                <has_text text="alt_org" />
                <has_text text="test_organism" />
                <has_text text="Testus" />
            </assert_contents>
        </output>
      </test>
  </tests>
  <help><![CDATA[
**What it does**

Lists organism in Apollo

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