diff export.xml @ 3:d4ae83dedb14 draft

planemo upload for repository https://github.com/TAMU-CPT/galaxy-webapollo commit 4ac38d0b6dba1183f3e78eb5c224c7051064b4a5

--- a/export.xml	Tue May 03 13:48:11 2016 -0400
+++ b/export.xml	Thu Jan 12 11:52:28 2017 -0500
@@ -1,32 +1,41 @@
 <?xml version="1.0"?>
-<tool id="edu.tamu.cpt2.webapollo.export" name="WA2: Retrieve/Export data" version="1.4">
-  <description>from WebApollo into Galaxy</description>
+<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
 
-@AUTH@
+@ADMIN_AUTH@
+
+@ORG_CN_OR_GUESS@
 
-@CN_OR_GUESS@
-
---gff $gff_out
---fasta $fasta_out
+--gff "$gff_out"
+--fasta "$fasta_out"
+--json "$json_out"
 
 ]]></command>
   <inputs>
     <expand macro="cn_or_guess" />
   </inputs>
   <outputs>
-    <data format="gff3" name="gff_out" />
-    <data format="fasta" name="fasta_out"/>
+    <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 GFF3/Fasta sequence from WebApollo.
+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>