diff variant.xml @ 1:43388fc8ad0b draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"

--- a/variant.xml	Sat May 23 13:36:47 2020 -0400
+++ b/variant.xml	Thu May 28 02:38:34 2020 -0400
@@ -7,26 +7,26 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-        ## initialize
-        @REF_FASTA@
+## initialize
+@REF_FASTA@
 
-        ## run
-        medaka variant
-        ## optional
-        --debug
-        #if $region
-            --region '${region}'
-        #end if
-        $verbose
-        ## required
-        'reference.fa'
-        #for $current in $inputs
-            '$current'
-        #end for
-        'result.vcf' ## output
+## run
+medaka variant
+## optional
+--debug
+#if $region
+    --region '${region}'
+#end if
+$verbose
+## required
+reference.fa
+#for $current in $inputs
+    '$current'
+#end for
+'$out_result' ## output
 
-        |& tee log.txt
-        ]]></command>
+|& tee '$out_log'
+    ]]></command>
     <inputs>
         <param argument="inputs" type="data" format="h5" multiple="true" label="Select consensus file(s)"/>
         <expand macro="reference"/>
@@ -39,11 +39,11 @@
     </inputs>
     <outputs>
         <!-- standard -->
-        <data name="out_result" format="vcf" from_work_dir="result.vcf" label="${tool.name} on ${on_string}: Result">
+        <data name="out_result" format="vcf" label="${tool.name} on ${on_string}: Result">
             <filter>'result' in out</filter>
         </data>
         <!-- optional -->
-        <data name="out_log" format="tabular" from_work_dir="log.txt" label="${tool.name} on ${on_string}: Log">
+        <data name="out_log" format="tabular" label="${tool.name} on ${on_string}: Log">
             <filter>'log' in out</filter>
         </data>
     </outputs>