# HG changeset patch
# User iuc
# Date 1590647934 14400
# Node ID 12c40c8c86dbb98e48c4771317168c514b30c18e
# Parent  0632744d5a5f6db9d52679fef9a26eff5a98581b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit e5b495e8ace37eaf31a3430a29de11c83416dc2c"

diff -r 0632744d5a5f -r 12c40c8c86db consensus.xml
--- a/consensus.xml	Sat May 23 13:37:18 2020 -0400
+++ b/consensus.xml	Thu May 28 02:38:54 2020 -0400
@@ -1,4 +1,4 @@
-<tool id="medaka_consensus" name="medaka: Consensus" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@">
+<tool id="medaka_consensus" name="medaka: Consensus" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
     <description>Assembly polishing via neural networks</description>
     <macros>
         <import>macros.xml</import>
@@ -6,45 +6,45 @@
     <expand macro="requirements"/>
     <expand macro="version_command"/>
     <command detect_errors="exit_code"><![CDATA[
-        ## initialize
-        ln -s '${bam}' 'alignment.bam' &&
-        ln -s '${bam.metadata.bam_index}' 'alignment.bam.bai' &&
+## initialize
+ln -s '${bam}' alignment.bam &&
+ln -s '${bam.metadata.bam_index}' alignment.bam.bai &&
 
-        ## run
-        medaka consensus
-        ## optional
-        --debug ## increase log level
-        --threads \${GALAXY_SLOTS:-4}
-        --batch_size $batch_size
-        #if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed'
-            --regions 
-            #if $regions_cond.regions_sel == 'custom'
-                '$regions_cond.custom'
-            #else if $regions_cond.regions_sel == 'bed'
-                '$regions_cond.bed'
-            #end if
-        #end if
-        --chunk_len $chunk_len
-        --chunk_ovlp $chunk_ovlp
-        --model '$model'
-        $disable_cudnn
-        $check_output
-        $save_features
-        #if $RG
-            --RG '$RG'
-        #end if
-        #if $tag_name
-            --tag_name '$tag_name'
-        #end if
-        #if $tag_value
-            --tag_value $tag_value
-        #end if
-        $tag_keep_missing
-        ## required
-        'alignment.bam' ## bam
-        'result.hdf' ## output
+## run
+medaka consensus
+## optional
+--debug ## increase log level
+--threads \${GALAXY_SLOTS:-4}
+--batch_size $batch_size
+#if $regions_cond.regions_sel == 'custom' or $regions_cond.regions_sel == 'bed'
+    --regions
+    #if $regions_cond.regions_sel == 'custom'
+        '$regions_cond.custom'
+    #else if $regions_cond.regions_sel == 'bed'
+        '$regions_cond.bed'
+    #end if
+#end if
+--chunk_len $chunk_len
+--chunk_ovlp $chunk_ovlp
+--model $model
+$disable_cudnn
+$check_output
+$save_features
+#if $RG
+    --RG '$RG'
+#end if
+#if $tag_name
+    --tag_name '$tag_name'
+#end if
+#if str($tag_value):
+    --tag_value $tag_value
+#end if
+$tag_keep_missing
+## required
+alignment.bam ## bam
+'$out_result' ## output
 
-        |& tee 'log.txt'
+|& tee '$out_log'
     ]]></command>
     <inputs>
         <param argument="bam" type="data" format="bam" label="Select input alignment"/>
@@ -56,13 +56,13 @@
                 <option value="custom">Custom input</option>
                 <option value="bed">BED file</option>
             </param>
+            <when value="none"/>
             <when value="custom">
-                <param argument="custom" type="text" value="" optional="true" label="Set genomic regions to analyse"/>
+                <param argument="custom" type="text" value="" label="Set genomic regions to analyse"/>
             </when>
             <when value="bed">
-                <param argument="bed" type="data" format="bed" optional="true" label="Select file with genomic regions to analyse"/>
+                <param argument="bed" type="data" format="bed" label="Select file with genomic regions to analyse"/>
             </when>
-            <when value="none"/>
         </conditional>
         <param argument="--chunk_len" type="integer" value="10000" label="Set chunk length of samples"/>
         <param argument="--chunk_ovlp" type="integer" value="1000" label="Set overlap of chunks"/>
@@ -80,11 +80,11 @@
     </inputs>
     <outputs>
         <!-- standard -->
-        <data name="out_result" format="h5" from_work_dir="result.hdf" label="${tool.name} on ${on_string}: Result">
+        <data name="out_result" format="h5" label="${tool.name} on ${on_string}: Result">
             <filter>'result' in out</filter>
         </data>
         <!-- optional -->
-        <data name="out_log" format="txt" label="${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>
diff -r 0632744d5a5f -r 12c40c8c86db macros.xml
--- a/macros.xml	Sat May 23 13:37:18 2020 -0400
+++ b/macros.xml	Thu May 28 02:38:54 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 0632744d5a5f -r 12c40c8c86db test-data/variants.vcf.gz
Binary file test-data/variants.vcf.gz has changed
diff -r 0632744d5a5f -r 12c40c8c86db tool_data_table_conf.xml.sample
--- a/tool_data_table_conf.xml.sample	Sat May 23 13:37:18 2020 -0400
+++ b/tool_data_table_conf.xml.sample	Thu May 28 02:38:54 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>