--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/guppy_basecaller.xml	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,30 @@
+<tool id="guppy-basecaller" name="Guppy basecaller wrapper" version="0.1.0" python_template_version="3.5">
+    <description>A simple wrapper for guppy basecaller that depends on configuration files</description>
+    <requirements>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        ln -s $infile input.fast5 &&
+        tar xf $config &&
+        guppy_basecaller -i . -s out -d . -c *.cfg
+    ]]></command>
+    <inputs>
+        <param name="infile" type="data" format="h5" label="Fast5 input"/>
+        <param name="config" type="data" format="tar" label="Guppy basecall configuration model"/>
+    </inputs>
+    <outputs>
+        <data name="results" format="fastq">
+            <discover_datasets directory="out" ext="fastq" pattern=".+\.fastq" visible="true"/>
+        </data>
+    </outputs>
+    <help><![CDATA[
+        A wrapper for guppy basecaller. This expects two inputs: a fast5 file, and a configuration in the form of a tar file. 
+
+        You can find configurations at https://github.com/nanoporetech/rerio, and in particular the directory https://github.com/nanoporetech/rerio/basecall_models. 
+
+        Each file there contains a URL you can download to use, for example https://github.com/nanoporetech/rerio/blob/master/basecall_models/res_rna2_r941_min_flipflop_v001 points to 'https://nanoporetech.box.com/shared/static/84e1jeudx8lr8ay7e9u1ebnvx3bk2kjf.tgz'
+
+        When uploading these .tgz files take care to set the format to 'tar' (galaxy doesn't autodetect this?).
+
+        The result should be a fastq file.
+    ]]></help>
+</tool>
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