--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Mon Sep 11 05:47:07 2017 -0400
@@ -0,0 +1,129 @@
+<?xml version="1.0"?>
+<macros>
+  <xml name="requirements">
+    <requirements>
+      <requirement type="package" version="2.7">python</requirement>
+      <requirement type="package" version="1.65">biopython</requirement>
+      <requirement type="package" version="0.6.2">bcbiogff</requirement>
+      <requirement type="package" version="2.12.4">requests</requirement>
+      <requirement type="package" version="0.16.0">future</requirement>
+      <yield/>
+    </requirements>
+  </xml>
+  <token name="@DATA_DIR@">\$GALAXY_SHARED_DIR</token>
+  <token name="@EXT_URL@">
+"\$GALAXY_WEBAPOLLO_EXT_URL"
+  </token>
+  <token name="@URL@">
+"\$GALAXY_WEBAPOLLO_URL"
+  </token>
+  <token name="@ADMIN_AUTH@">
+"\$GALAXY_WEBAPOLLO_URL"
+"\$GALAXY_WEBAPOLLO_USER"
+"\$GALAXY_WEBAPOLLO_PASSWORD"
+  </token>
+
+  <token name="@ORG_OR_GUESS@">
+<![CDATA[
+#if $org_source.source_select == "auto_json":
+    --org_json "${org_source.org_file}"
+#elif $org_source.source_select == "select":
+    --org_id "${org_source.org_select}"
+#else:
+    --org_raw "${org_source.org_raw}"
+#end if
+]]>
+  </token>
+  <token name="@ORG_CN_OR_GUESS@">
+<![CDATA[
+@ORG_OR_GUESS@
+
+#if $cn_source.source_select == "auto":
+    #if str($cn_source.cn_file) != "None":
+        --seq_fasta $cn_source.cn_file
+    #end if
+#else
+    #if $cn_source.source_select != "all" and len($cn_source.refseqs) > 0:
+        --seq_raw
+        #for $item in $cn_source.refseqs:
+            "${item.refseq}"
+        #end for
+    #end if
+#end if
+]]>
+  </token>
+  <xml name="org_or_guess">
+    <conditional name="org_source">
+        <param name="source_select" type="select" label="Organism Common Name Source">
+            <option value="select">Select</option>
+            <option value="direct">Direct Entry</option>
+            <option value="auto_json">Autodetect from Apollo JSON</option>
+        </param>
+        <when value="select">
+            <param name="org_select" type="select" dynamic_options="galaxy_list_orgs(__trans__)" label="Organism" />
+        </when>
+        <when value="direct">
+            <param name="org_raw" type="text" label="Organism Common Name" optional="False" />
+        </when>
+        <when value="auto_json">
+            <param name="org_file" type="data" format="json" label="Apollo Organism File" help="Will only fetch first organism" />
+        </when>
+    </conditional>
+  </xml>
+  <xml name="cn_or_guess">
+    <expand macro="org_or_guess" />
+    <conditional name="cn_source">
+        <param name="source_select" type="select" label="Organism Sequence(s) Source">
+            <option value="all">All Refseqs</option>
+            <option value="direct">Direct Entry</option>
+            <option value="auto">Autodetect from Fasta</option>
+        </param>
+        <when value="all">
+        </when>
+        <when value="auto">
+            <param name="cn_file" type="data" format="fasta" label="Reference sequence(s)" optional="true"/>
+        </when>
+        <when value="direct">
+            <repeat name="refseqs" title="Reference Sequences" help="These are used to identify sequences within an organism that you wish to extract">
+                <param name="refseq" type="text" label="Reference sequence(s)" />
+            </repeat>
+        </when>
+    </conditional>
+  </xml>
+
+  <xml name="test_result">
+      <assert_stderr>
+          <has_text text="MissingSchema" />
+      </assert_stderr>
+  </xml>
+
+  <xml name="citations">
+      <citations>
+      </citations>
+  </xml>
+  <xml name="gff3_input">
+    <param label="GFF3 Annotations" name="gff3_data" type="data" format="gff3"/>
+  </xml>
+  <token name="@GENOME_SELECTOR_PRE@">
+#if $reference_genome.reference_genome_source == 'history':
+    ln -s $reference_genome.genome_fasta genomeref.fa;
+#end if
+  </token>
+  <token name="@GENOME_SELECTOR@">
+#if $reference_genome.reference_genome_source == 'cached':
+    "${reference_genome.fasta_indexes.fields.path}"
+#elif $reference_genome.reference_genome_source == 'history':
+    genomeref.fa
+#end if
+  </token>
+<token name="@REFERENCES@">
+<![CDATA[
+------
+
+**Citation**
+
+If you use this tool in Galaxy, please cite:
+Eric Rasche (2016), `Galaxy Apollo Tools <https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/apollo>`_
+]]>
+    </token>
+</macros>