# HG changeset patch
# User iuc
# Date 1590647975 14400
# Node ID 551f8c9bc4cfe4950f8e5eb39b677d5ba1f23e43
# Parent  ef94bace3a3c825e8cef65eccecca9b818abf8fb
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"

diff -r ef94bace3a3c -r 551f8c9bc4cf macros.xml
--- a/macros.xml	Sat May 23 13:38:26 2020 -0400
+++ b/macros.xml	Thu May 28 02:39:35 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 ef94bace3a3c -r 551f8c9bc4cf medaka_consensus.xml
--- a/medaka_consensus.xml	Sat May 23 13:38:26 2020 -0400
+++ b/medaka_consensus.xml	Thu May 28 02:39:35 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="medaka_consensus_pipeline" name="medaka: Consensus pipeline" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>Assembly polishing via neural networks</description>
     <macros>
         <import>macros.xml</import>
@@ -6,23 +6,20 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-        medaka_consensus
-        ## optional
-        -m '${m}'
-        -b $b
-        -o 'results'
-        #if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',')
-            -v
-        #end if
-        -t \${GALAXY_SLOTS:-4}
-        ## required
-        -i '$i'
-        -d '$d'
+medaka_consensus
+## optional
+-m ${m}
+-b $b
+-o results
+#if 'draft' in str($out).split(',') or 'variants' in str($out).split(',') or 'polished' in str($out).split(',')
+    -v
+#end if
+-t \${GALAXY_SLOTS:-4}
+## required
+-i '$i'
+-d '$d'
 
-        |& tee 'log.txt'
-        #if 'variants' in str($out).split(',')
-            && bgzip -d 'results/variants.vcf.gz'
-        #end if
+|& tee '$out_log'
     ]]></command>
     <inputs>
         <param argument="-i" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz" label="Select basecalls"/>
@@ -54,14 +51,14 @@
         <data name="out_draft" format="txt" from_work_dir="results/draft_to_consensus.chain" label="${tool.name} on ${on_string}: Draft to consensus">
             <filter>'draft' in out</filter>
         </data>
-        <data name="out_variants" format="vcf" from_work_dir="results/variants.vcf" label="${tool.name} on ${on_string}: Variants">
+        <data name="out_variants" format="vcf_bgzip" from_work_dir="results/variants.vcf.gz" label="${tool.name} on ${on_string}: Variants">
             <filter>'variants' in out</filter>
         </data>
         <data name="out_polished" format="bed" from_work_dir="results/polished_regions_in_draft_coords.bed" label="${tool.name} on ${on_string}: Polished regions in Draft">
             <filter>'polished' in out</filter>
         </data>
         <!-- optional -->
-        <data name="out_log" format="txt" label="${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>
@@ -124,13 +121,7 @@
                     <has_size value="9"/>
                 </assert_contents>
             </output>
-            <output name="out_variants">
-                <assert_contents>
-                    <has_n_lines n="9"/>
-                    <has_line line="##fileformat=VCFv4.1"/>
-                    <has_text_matching expression="4&#009;.+"/>
-                </assert_contents>
-            </output>
+            <output name="out_variants" file="variants.vcf.gz" decompress="true"/>
             <output name="out_log">
                 <assert_contents>
                     <has_line line="Polished assembly written to results/consensus.fasta, have a nice day."/>
diff -r ef94bace3a3c -r 551f8c9bc4cf test-data/variants.vcf.gz
Binary file test-data/variants.vcf.gz has changed
diff -r ef94bace3a3c -r 551f8c9bc4cf tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sat May 23 13:38:26 2020 -0400
+++ b/tool_data_table_conf.xml.sample	Thu May 28 02:39:35 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>