diff manta_macros.xml @ 3:d648e40c6da9 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/manta commit 3b3617515f0e59c35849939c26e4891f02c4de0b"

--- a/manta_macros.xml	Sun Jun 07 09:08:06 2020 -0400
+++ b/manta_macros.xml	Sun Jun 07 16:43:54 2020 -0400
@@ -1,14 +1,14 @@
 <macros>
 
     <token name="@VERSION@">1.6</token>
-    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy4</token>
+    <token name="@WRAPPER_VERSION@">@VERSION@+galaxy5</token>
     <token name="@pipefail@"><![CDATA[set -o | grep -q pipefail && set -o pipefail;]]></token>
 
     <token name="@set_reference_fasta_filename@"><![CDATA[
     #set $reference_fasta_filename = "localref.fa"
 
     #if str( $reference_source.reference_source_selector ) == "history":
-    ln -s -f '${reference_source.ref_file}' '${reference_fasta_filename}' &&
+    ln -s '${reference_source.ref_file}' '${reference_fasta_filename}' &&
     samtools faidx '${reference_fasta_filename}' 2>&1 || echo "Error running samtools faidx for Manta" >&2 &&
     #else:
     #set $reference_fasta_filename = str( $reference_source.index.fields.path )
@@ -21,7 +21,7 @@
     #else if str( $configuration.configuration_switch )== "Customized":
     #set $config_file = '$configuration.Customized'
     #else:
-    #set $config_file = $__tool_directory__ + '/configManta.py.ini'
+    #set $config_file = 'configManta.py.ini'
     #end if
     ]]></token>