changeset 4:cd06929b224b draft

"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/racon commit f88d0f555d2bb239e6f2818454fc767ccd2f2150"

--- a/macros.xml	Sat Apr 18 19:39:13 2020 -0400
+++ b/macros.xml	Sun Aug 29 10:49:02 2021 +0000
@@ -1,11 +1,12 @@
 <macros>
     <xml name="requirements">
         <requirements>
-        <requirement type="package" version="@VERSION@">racon</requirement>
+        <requirement type="package" version="@TOOL_VERSION@">racon</requirement>
             <yield/>
         </requirements>
     </xml>
-    <token name="@VERSION@">1.4.13</token>
+    <token name="@TOOL_VERSION@">1.4.13</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1101/gr.214270.116</citation>

--- a/racon.xml	Sat Apr 18 19:39:13 2020 -0400
+++ b/racon.xml	Sun Aug 29 10:49:02 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="racon" name="Racon" version="@VERSION@">
+<tool id="racon" name="Racon" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
     <description>Consensus module for raw de novo DNA assembly of long uncorrected reads.</description>
     <macros>
         <import>macros.xml</import>
@@ -6,22 +6,40 @@
     <expand macro="requirements" />
     <version_command>racon --version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-        ln -s '$reads' reads.${reads.ext} && 
+        #if $reads.ext.startswith("fasta")
+            #set ext="fasta"
+        #else
+            #set ext="fastq"
+        #end if
+        #if $reads.ext.endswith(".gz")
+            #set ext=ext+".gz"
+        #end if
+       
+        ln -s '$reads' reads.$ext && 
         #if $overlaps.ext == 'sam':
             ln -s '$overlaps' overlaps.${overlaps.ext} && 
         #else:
             ln -s '$overlaps' overlaps.paf &&
         #end if
-        ln -s '$corrected_reads' corrected_reads.${corrected_reads.ext} && 
+  
+        #if $corrected_reads.ext.startswith("fasta")
+            #set cext="fasta"
+        #else
+            #set cext="fastq"
+        #end if
+        #if $corrected_reads.ext.endswith(".gz")
+            #set cext=cext+".gz"
+        #end if
+        ln -s '$corrected_reads' corrected_reads.$cext && 
 
         racon 
-            reads.${reads.ext}
+            reads.$ext
             #if $overlaps.ext == 'sam':
                 overlaps.${overlaps.ext}
             #else:
                 overlaps.paf
             #end if
-            corrected_reads.${corrected_reads.ext}
+            corrected_reads.$cext
             -t \${GALAXY_SLOTS:-4} 
             $u
             $f