# HG changeset patch
# User iuc
# Date 1590647914 14400
# Node ID 43388fc8ad0b36e9b39f88487ffa795a01ef946c
# Parent  3cde72a6e37c18c5ba87df8f2b2beeb65a03f3a7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"

diff -r 3cde72a6e37c -r 43388fc8ad0b macros.xml
--- a/macros.xml	Sat May 23 13:36:47 2020 -0400
+++ b/macros.xml	Thu May 28 02:38:34 2020 -0400
@@ -22,20 +22,20 @@
         </citations>
     </xml>
 
-    <!-- 
+    <!--
         command
     -->
 
-    <token name="@REF_FASTA@"><![CDATA[        
+    <token name="@REF_FASTA@"><![CDATA[
         #if $reference_source.reference_source_selector == 'history':
-            ln -f -s '$reference_source.ref_file' 'reference.fa' &&
+            ln -f -s '$reference_source.ref_file' reference.fa &&
         #else:
-            ln -f -s '$reference_source.ref_file.fields.path' 'reference.fa' &&
+            ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
         #end if
     ]]></token>
 
     <!--
-        input 
+        input
     -->
 
     <xml name="b" token_argument="-b">
diff -r 3cde72a6e37c -r 43388fc8ad0b test-data/variants.vcf.gz
Binary file test-data/variants.vcf.gz has changed
diff -r 3cde72a6e37c -r 43388fc8ad0b tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sat May 23 13:36:47 2020 -0400
+++ b/tool_data_table_conf.xml.sample	Thu May 28 02:38:34 2020 -0400
@@ -4,4 +4,4 @@
         <columns>value, dbkey, name, path</columns>
         <file path="all_fasta.loc" />
     </table>
-</tables>
\ No newline at end of file
+</tables>
diff -r 3cde72a6e37c -r 43388fc8ad0b variant.xml
--- 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>