--- a/medaka_variant.xml	Sat May 23 13:37:48 2020 -0400
+++ b/medaka_variant.xml	Thu May 28 02:39:16 2020 -0400
@@ -6,32 +6,32 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-        ## initialize
-        @REF_FASTA@  
-        ## link doesn't work
-        cp '${i}' 'alignment.bam' &&
-        cp '${i.metadata.bam_index}' 'alignment.bam.bai' &&
+## initialize
+@REF_FASTA@
+## link doesn't work
+cp '${i}' alignment.bam &&
+cp '${i.metadata.bam_index}' alignment.bam.bai &&
 
-        ## run
-        medaka_variant
-        ## optional
-        #if str($r) != ''
-            -r '$r'
-        #end if
-        -o 'results'
-        -s '$s'
-        -m '$m'
-        -t \${GALAXY_SLOTS:-4}
-        -b $b
-        -N $N
-        -P $P
-        $U
-        $S
-        ## required
-        -i 'alignment.bam'
-        -f 'reference.fa'
+## run
+medaka_variant
+## optional
+#if $r:
+    -r '$r'
+#end if
+-o results
+-s $s
+-m $m
+-t \${GALAXY_SLOTS:-4}
+-b $b
+-N $N
+-P $P
+$U
+$S
+## required
+-i alignment.bam
+-f reference.fa
 
-        |& tee 'log.txt'
+|& tee '$out_log'
     ]]></command>
     <inputs>
         <param argument="-i" type="data" format="bam" label="Select input reads" help="Read groups are currently ignored, so the bam should only contain reads from a single sample."/>
@@ -92,7 +92,7 @@
         <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf">
             <filter>'round_1_unfiltered_vcf' in out</filter>
         </data>
-        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt">
+        <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
             <filter>'log' in out</filter>
         </data>
     </outputs>