# HG changeset patch
# User dfornika
# Date 1583887686 0
# Node ID eecb8c89113477b500d6c4f45cff7b2abe77e0f7

"planemo upload for repository https://github.com/public-health-bioinformatics/galaxytools/tree/master/tools/medaka commit 54b753ab7f1805cdef74b8eac46cbe4fa039c9b6-dirty"

diff -r 000000000000 -r eecb8c891134 medaka_consensus.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/medaka_consensus.xml	Wed Mar 11 00:48:06 2020 +0000
@@ -0,0 +1,48 @@
+<tool id="medaka_consensus" name="medaka_consensus" version="@VERSION@" profile="19.01">
+    <description>Creates a consensus sequence from an alignment generated from nanopore sequence data</description>
+    <macros>
+        <token name="@VERSION@">0.11.5</token>
+    </macros>
+    <requirements>
+        <requirement type="package" version="@VERSION@">medaka</requirement>
+        <requirement type="package" version="1.9">samtools</requirement>
+    </requirements>
+    <version_command>medaka --version</version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s '${input_alignment}' alignment.bam &&
+        samtools index alignment.bam &&
+        medaka consensus 
+          --threads \${GALAXY_SLOTS:-4}
+          --model '${model}'
+          alignment.bam
+          '${consensus_hdf}'
+          > '${log}'
+    ]]></command>
+    <inputs>
+        <param name="input_alignment" type="data" format="bam" label="Input Alignment"/>
+        <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>
+        <data name="consensus_hdf" format="binary" label="${tool.name} on ${on_string}: consensus hdf" />
+        <data name="log" format="txt" label="${tool.name} on ${on_string}: Log" from_work_dir="log.txt"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help><![CDATA[
+    ]]></help>
+</tool>
diff -r 000000000000 -r eecb8c891134 test-data/res.hdf
Binary file test-data/res.hdf has changed
diff -r 000000000000 -r eecb8c891134 test-data/res.primertrimmed.sorted.bam
Binary file test-data/res.primertrimmed.sorted.bam has changed
diff -r 000000000000 -r eecb8c891134 test-data/res.primertrimmed.sorted.bam.bai
Binary file test-data/res.primertrimmed.sorted.bam.bai has changed