diff snpEff_macros.xml @ 25:5c7b70713fb5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit a4c17efb8ec4b3a315766f5b5602effa275fade3

--- a/snpEff_macros.xml	Wed Oct 13 23:30:29 2021 +0000
+++ b/snpEff_macros.xml	Wed Aug 03 16:33:45 2022 +0000
@@ -18,6 +18,22 @@
   <token name="@SNPEFF_VERSION@">SnpEff4.3</token>
   <token name="@SNPEFF_DATABASE_URL@">https://sourceforge.net/projects/snpeff/files/databases/v4_3/</token>
   <token name="@JAVA_OPTIONS@">-Xmx\${GALAXY_MEMORY_MB:-8192}m</token>
+  <xml name="ref_select">
+    <conditional name="reference_source">
+        <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+            <option value="cached">Locally cached</option>
+            <option value="history">History</option>
+        </param>
+        <when value="cached">
+            <param name="ref_file" type="select" label="Select reference genome">
+                <options from_data_table="fasta_indexes"/>
+            </param>
+        </when>
+        <when value="history">
+            <param name="input_fasta" type="data" format="fasta,fasta.gz" label="Genome in FASTA format" help="This dataset is required for generating SnpEff database. See help section below."/>
+        </when>
+    </conditional>
+  </xml>
   <token name="@EXTERNAL_DOCUMENTATION@">