# HG changeset patch
# User iuc
# Date 1592471252 14400
# Node ID 6a87478ed985253ec951e8bd974b9f41c9013f3c
# Parent  551f8c9bc4cfe4950f8e5eb39b677d5ba1f23e43
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7fec11af843c91c70413844368c1d5f5f78ce45e"

diff -r 551f8c9bc4cf -r 6a87478ed985 macros.xml
--- a/macros.xml	Thu May 28 02:39:35 2020 -0400
+++ b/macros.xml	Thu Jun 18 05:07:32 2020 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <macros>
-    <token name="@TOOL_VERSION@">1.0.1</token>
+    <token name="@TOOL_VERSION@">1.0.3</token>
     <token name="@PROFILE@">18.01</token>
     <xml name="requirements">
         <requirements>
@@ -55,13 +55,13 @@
             <option value="r941_min_high_g330">r941_min_high_g330</option>
             <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
             <option value="r941_min_high_g344">r941_min_high_g344</option>
-            <option value="r941_min_high_g351" selected="true">r941_min_high_g351</option>
+            <option value="r941_min_high_g351">r941_min_high_g351</option>
             <option value="r941_min_high_g360">r941_min_high_g360</option>
             <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
             <option value="r941_prom_high_g303">r941_prom_high_g303</option>
             <option value="r941_prom_high_g330">r941_prom_high_g330</option>
             <option value="r941_prom_high_g344">r941_prom_high_g344</option>
-            <option value="r941_prom_high_g360">r941_prom_high_g360</option>
+            <option value="r941_prom_high_g360" selected="true">r941_prom_high_g360</option>
             <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
             <option value="r941_prom_snp_g322">r941_prom_snp_g322</option>
             <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
@@ -77,14 +77,14 @@
             <when value="cached">
                 <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
                     <options from_data_table="all_fasta">
-                        <filter type="sort_by" column="2" />
-                        <validator type="no_options" message="No reference genomes are available" />
+                        <filter type="sort_by" column="2"/>
+                        <validator type="no_options" message="No reference genomes are available"/>
                     </options>
                     <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                 </param>
             </when>
             <when value="history">
-                <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference" />
+                <param name="ref_file" type="data" format="fasta,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
             </when>
         </conditional>
     </xml>
@@ -94,11 +94,11 @@
     -->
 
     <token name="@WID@"><![CDATA[
-medaka is a tool suite to create a consensus sequence from nanopore sequencing data.
+*medaka* is a tool suite to create a consensus sequence from nanopore sequencing data.
 
 This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly. It outperforms graph-based methods operating on basecalled data, and can be competitive with state-of-the-art signal-based methods, whilst being much faster.
     ]]></token>
     <token name="@REFERENCES@"><![CDATA[
 More information are available in the `manual <https://nanoporetech.github.io/medaka/index.html>`_ and `github <https://github.com/nanoporetech/medaka>`_.
     ]]></token>
-</macros>
+</macros>
\ No newline at end of file
diff -r 551f8c9bc4cf -r 6a87478ed985 medaka_consensus.xml
--- a/medaka_consensus.xml	Thu May 28 02:39:35 2020 -0400
+++ b/medaka_consensus.xml	Thu Jun 18 05:07:32 2020 -0400
@@ -76,12 +76,12 @@
             </output>
             <output name="out_probs">
                 <assert_contents>
-                    <has_size value="194782" delta="100"/>
+                    <has_size value="192187" delta="100"/>
                 </assert_contents>
             </output>
             <output name="out_calls">
                 <assert_contents>
-                    <has_size value="533139" delta="100"/>
+                    <has_size value="533242" delta="100"/>
                 </assert_contents>
             </output>
         </test>
diff -r 551f8c9bc4cf -r 6a87478ed985 test-data/variants.vcf.gz
Binary file test-data/variants.vcf.gz has changed