diff lastz_macros.xml @ 7:10aca14c2332 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/lastz commit 13e9724b44888b0de9535ac7b561ad9686038413

--- a/lastz_macros.xml	Fri Mar 02 12:07:00 2018 -0500
+++ b/lastz_macros.xml	Thu May 17 04:29:13 2018 -0400
@@ -1,11 +1,26 @@
 <macros>
     <token name="@LASTZ_CONDA_VERSION@">1.0.4</token>
-    <token name="@TARGET_INPUT_COMMAND_LINE@">
+    <token name="@TARGET_INPUT_COMMAND_LINE@"><![CDATA[
         #if $source.ref_source=="history":
-            '${source.target}'
+            #if $source.target.is_of_type('fasta.gz'):
+                <(gunzip -c '${source.target}')
+            #else:
+                '${source.target}'
+            #end if
         #else:
             '${source.target_2bit.fields.path}'
         #end if
+        ]]>
+    </token>
+    <token name="@query_input@"><![CDATA[
+        #if $query.is_of_type('fasta.gz','fastq.gz'):
+            <(gunzip -c '${query}')
+        #elif $query.is_of_type('fastq.bz2'):
+            <(bunzip2 -c '${query}')
+        #else:
+            '${query}'
+        #end if
+        ]]>
     </token>
     <xml name="target_input">
         <conditional name="source">
@@ -19,7 +34,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="target" type="data" format="fasta" label="Select a reference dataset" />
+                <param name="target" type="data" format="fasta,fasta.gz" label="Select a reference dataset" />
             </when>
         </conditional>
     </xml>