racon: fix file extensions (#1149)

* racon: fix file extensions must be fastq/fasta but they aren't for fastqsanger ... fixes galaxyproject/tools-iuc#3856 * racond: bump version
bgruening · Aug 29, 2021 · f88d0f5 · f88d0f5
1 parent d30c91c
commit f88d0f5
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Showing 2 changed files with 26 additions and 7 deletions.
diff --git a/tools/racon/macros.xml b/tools/racon/macros.xml
@@ -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>

diff --git a/tools/racon/racon.xml b/tools/racon/racon.xml
@@ -1,27 +1,45 @@
-<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>
     </macros>
     <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