Mercurial > repos > iuc > stacks2_refmap

diff stacks_refmap.xml @ 1:e1f99efbfd81 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/stacks2 commit c300b84615660459bb0020fa74ccd3b874d329a4"
author iuc
date Mon, 30 Sep 2019 13:59:21 -0400
parents 524bd85b0bec
children 6e43ea81f086
line wrap: on
line diff
--- a/stacks_refmap.xml	Mon Jul 01 10:54:35 2019 -0400
+++ b/stacks_refmap.xml	Mon Sep 30 13:59:21 2019 -0400
@@ -7,7 +7,12 @@
     <expand macro="version_cmd"/>
     <command detect_errors="aggressive"><![CDATA[
 @FASTQ_INPUT_FUNCTIONS@
-mkdir bam_inputs stacks_outputs&&
+mkdir bam_inputs stacks_outputs &&
+
+#if $output_log
+    ln -s '$output_log' stacks_outputs/ref_map.log &&
+#end if
+
 @BAM_INPUT@
 
 ref_map.pl
@@ -22,10 +27,6 @@
 --gt-alpha $model_options.gt_alpha
 
 @EXTRACT_VCF@
-
-#if $output_log
-    && mv stacks_outputs/ref_map.log $output_log
-#end if
     ]]></command>
 
     <inputs>