diff macros.xml @ 1:1d4f065fa0ef draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/irissv/ commit e3ffd8ae7c25536658ff3ee76389f0c2a9894b4c"

--- a/macros.xml	Tue Jan 19 20:30:21 2021 +0000
+++ b/macros.xml	Mon May 17 17:29:39 2021 +0000
@@ -1,7 +1,7 @@
 <?xml version="1.0"?>
 <macros>
     <token name="@TOOL_VERSION@">1.0.4</token>
-    <token name="@PROFILE@">18.01</token>
+    <token name="@PROFILE@">20.01</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="1.9">samtools</requirement>
@@ -29,9 +29,16 @@
 
     <token name="@REF_FASTA@"><![CDATA[
         #if $reference_source.reference_source_selector == 'history':
-            ln -f -s '$reference_source.ref_file' reference.fa &&
+            #set reference = $reference_source.ref_file
+            #set ext = $reference.ext
         #else:
-            ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
+            #set reference = $reference_source.ref_file.fields.path
+            #set ext = $reference_source.ref_file.fields.path
+        #end if
+        #if $ext.endswith('.gz'):
+            gunzip -c '$reference' > reference &&
+        #else:
+            ln -sf '$reference' reference &&
         #end if
     ]]></token>
 
@@ -51,7 +58,7 @@
                 </param>
             </when>
             <when value="history">
-                <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
+                <param name="ref_file" type="data" format="fasta,fasta.gz,fastq,fastq.gz" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
             </when>
         </conditional>
     </xml>