--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/medaka.xml	Sun Feb 23 09:04:41 2020 -0500
@@ -0,0 +1,69 @@
+<tool id="medaka_consensus" name="medaka_consensus" version="@VERSION@" profile="19.01">
+    <description> creates a consensus sequence from nanopore sequencing data</description>
+    <macros>
+        <token name="@VERSION@">0.11.5</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">medaka</requirement>
+    </requirements>
+    <version_command>medaka --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        medaka_consensus 
+        -i '${basecalled}' 
+        -d '${draft}' 
+        -o out_dir 
+        -t \${GALAXY_SLOTS:-4} 
+        -m '${model}' > log.txt
+    ]]>    </command>
+
+    <inputs>
+        <param name="basecalled" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz,fasta,fasta.gz"
+            label="Basecalled data"/>
+        <param name="draft" type="data" format="fasta,fasta.gz" label="Draft assemblies"
+            help="The input assembly should be preprocessed with racon"/>
+        <param name="model" type="select" label="Model">
+            <option value="r941_min_fast_g303">r941_min_fast_g303</option>
+            <option value="r941_min_high_g303" selected="True">r941_min_high_g303</option>
+            <option value="r941_min_high_g330">r941_min_high_g330</option>
+            <option value="r941_min_high_g344">r941_min_high_g344</option>
+            <option value="r941_prom_fast_g303">r941_prom_fast_g303</option>
+            <option value="r941_prom_high_g303">r941_prom_high_g303</option>
+            <option value="r941_prom_high_g344">r941_prom_high_g344</option>
+            <option value="r941_prom_high_g330">r941_prom_high_g330</option>
+            <option value="r10_min_high_g303">r10_min_high_g303</option>
+            <option value="r10_min_high_g340">r10_min_high_g340</option>
+            <option value="r103_min_high_g345">r103_min_high_g345</option>
+            <option value="r941_prom_snp_g303">r941_prom_snp_g303</option>
+            <option value="r941_prom_variant_g303">r941_prom_variant_g303</option>
+            <option value="r941_min_high_g340_rle">r941_min_high_g340_rle</option>
+        </param>
+    </inputs>
+    <outputs>
+        <!-- <collection name="list_output" type="list" label="Output">
+        <discover_datasets pattern="__name_and_ext__" directory="out_dir"/>
+    </collection> -->
+        <data name="consensus" format="fasta" label="${tool.name} on ${on_string}: consensus" from_work_dir="out_dir/consensus.fasta"/>
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="draft" value="plasmid.fasta" />
+            <param name="basecalled" value="reads.fastq" />
+            <param name="model" value="r941_min_fast_g303"/>
+            <output name="consensus" file="medaka/consensus.fasta" ftype="fasta" />
+        </test>
+    </tests>
+    <help><![CDATA[
+
+.. class:: infomark
+
+**What it does**
+
+medaka is a tool 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.
+
+
+    ]]></help>
+</tool>