view export.xml @ 7:f9a6e151b3b4 draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 52b9e5bf6a6efb09a5cb845ee48703651c644174

<?xml version="1.0"?>
<tool id="edu.tamu.cpt2.webapollo.export" name="Retrieve Data" version="3.0">
  <description>from Apollo into Galaxy</description>
  <macros>
    <import>macros.xml</import>
  </macros>
  <code file="webapollo.py"/>
  <expand macro="requirements"/>
  <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"

]]></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"/>
  </outputs>
  <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>
</tool>