# HG changeset patch
# User iuc
# Date 1592471320 14400
# Node ID ce2bf68a260d9e275a1be6a6db887b828416d03c
# Parent  92cdc29a86207fee079cf494e513e70c130e06df
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/medaka commit 7fec11af843c91c70413844368c1d5f5f78ce45e"

diff -r 92cdc29a8620 -r ce2bf68a260d macros.xml
--- a/macros.xml	Thu May 28 02:39:16 2020 -0400
+++ b/macros.xml	Thu Jun 18 05:08:40 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 92cdc29a8620 -r ce2bf68a260d medaka_variant.xml
--- a/medaka_variant.xml	Thu May 28 02:39:16 2020 -0400
+++ b/medaka_variant.xml	Thu Jun 18 05:08:40 2020 -0400
@@ -22,6 +22,7 @@
 -s $s
 -m $m
 -t \${GALAXY_SLOTS:-4}
+-p
 -b $b
 -N $N
 -P $P
@@ -53,17 +54,18 @@
             <option value="round_1_hap_2_vcf">round_1_hap_2.vcf</option>
             <option value="round_1_hap_1_probs_hdf">round_1_hap_1_probs.hdf</option>
             <option value="round_1_hap_2_probs_hdf">round_1_hap_2_probs.hdf</option>
+            <option value="round_1_phased.vcf">round_1_phased.vcf</option>
             <option value="round_1_unfiltered_vcf">round_1_unfiltered.vcf</option>
             <option value="round_1_vcf" selected="true">round_1.vcf</option>
             <option value="log">Log</option>
         </param>
     </inputs>
     <outputs>
-        <!-- standard -->
+        <!-- standard output-->
         <data name="out_round_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1.vcf" from_work_dir="results/round_1.vcf">
             <filter>'round_1_vcf' in out</filter>
         </data>
-        <!-- optional -->
+        <!-- optional output: round 0 -->
         <data name="out_round_0_hap_mixed_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_0_hap_mixed_probs_hdf" from_work_dir="results/round_0_hap_mixed_probs.hdf">
             <filter>'round_0_hap_mixed_probs_hdf' in out</filter>
         </data>
@@ -76,7 +78,7 @@
         <data name="out_round_0_hap_mixed_unphased_vcf" format="vcf" label="${tool.name} on ${on_string}: round_0_hap_mixed_unphased_vcf" from_work_dir="results/round_0_hap_mixed_unphased.vcf">
             <filter>'round_0_hap_mixed_unphased_vcf' in out</filter>
         </data>
-        <!-- round 1 -->
+        <!-- optional output: round 1 -->
         <data name="out_round_1_hap_1_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_hap_1.vcf" from_work_dir="results/round_1_hap_1.vcf">
             <filter>'round_1_hap_1_vcf' in out</filter>
         </data>
@@ -89,9 +91,13 @@
         <data name="out_round_1_hap_2_probs_hdf" format="h5" label="${tool.name} on ${on_string}: round_1_hap_2_probs.hdf" from_work_dir="results/round_1_hap_2_probs.hdf">
             <filter>'round_1_hap_2_probs_hdf' in out</filter>
         </data>
+        <data name="out_round_1_phased.vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_phased.vcf" from_work_dir="results/round_1_phased.vcf">
+            <filter>'round_1_phased.vcf' in out</filter>
+        </data>
         <data name="out_round_1_unfiltered_vcf" format="vcf" label="${tool.name} on ${on_string}: round_1_unfiltered.vcf" from_work_dir="results/round_1_unfiltered.vcf">
             <filter>'round_1_unfiltered_vcf' in out</filter>
         </data>
+        <!-- optional output: log -->
         <data name="out_log" format="txt" label="${tool.name} on ${on_string}: Log">
             <filter>'log' in out</filter>
         </data>
@@ -141,6 +147,7 @@
 
 **Output**
 
+- round_0_hap_mixed_phased.bam
 - round_0_hap_mixed_phased.vcf
 - round_0_hap_mixed_probs.hdf
 - round_0_hap_mixed_unphased.vcf
@@ -148,8 +155,10 @@
 - round_1_hap_1.vcf
 - round_1_hap_2_probs.hdf
 - round_1_hap_2.vcf
+- round_1_phased.vcf
 - round_1_unfiltered.vcf
 - round_1.vcf
+- log
 
 **References**
 
diff -r 92cdc29a8620 -r ce2bf68a260d test-data/variants.vcf.gz
Binary file test-data/variants.vcf.gz has changed