diff export.xml @ 0:a5ebd72b4369 draft

planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo commit f745b23c84a615bf434d717c8c0e553a012f0268

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/export.xml	Mon Sep 11 05:35:58 2017 -0400
@@ -0,0 +1,55 @@
+<?xml version="1.0"?>
+<tool id="export" name="Retrieve Data" version="3.0">
+  <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"
+
+]]></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>
+  <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>