Merge pull request #5504 from mvdbeek/medaka_fix

Copy medaka fasta inputs
galaxyproject · Sep 26, 2023 · 7105600 · 7105600
2 parents c85c5d9 + 58ccdb1
commit 7105600
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Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/tools/medaka/macros.xml b/tools/medaka/macros.xml
@@ -1,6 +1,6 @@
 <macros>
     <token name="@TOOL_VERSION@">1.7.2</token>
-    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@VERSION_SUFFIX@">1</token>
     <token name="@PROFILE@">21.01</token>
     <xml name="bio_tools">
         <xrefs>
@@ -37,10 +37,10 @@
             #if $reference_source.ref_file.ext.endswith(".gz")
                 gunzip -c '$reference_source.ref_file' > reference.fa &&
             #else
-                ln -f -s '$reference_source.ref_file' reference.fa &&
+                cp '$reference_source.ref_file' reference.fa &&
             #end if
         #else:
-            ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
+            cp '$reference_source.ref_file.fields.path' reference.fa &&
         #end if
     ]]></token>
 

diff --git a/tools/medaka/snp.xml b/tools/medaka/snp.xml
@@ -140,6 +140,7 @@
 This module decodes probabilities to SNPs but NOT indels.
 
 For a more general solution see the medaka *variant* tool.
+
 ----
 
 .. class:: infomark
-Original file line number
+Diff line change
@@ Expand Up / @@ -140,6 +140,7 @@ @@
     This module decodes probabilities to SNPs but NOT indels.
     For a more general solution see the medaka *variant* tool.
     ----
     .. class:: infomark
@@ Expand Down @@