--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml	Sat May 23 13:38:26 2020 -0400
@@ -0,0 +1,104 @@
+<?xml version="1.0"?>
+<macros>
+    <token name="@TOOL_VERSION@">1.0.1</token>
+    <token name="@PROFILE@">18.01</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">medaka</requirement>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command>medaka --version</version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="bibtex">@online{medaka,
+              author = {Oxford Nanopore Technologies Ltd.},
+              title = {medaka},
+              year = 2020,
+              url = {https://github.com/nanoporetech/medaka},
+              urldate = {2020-05-06}
+            }</citation>
+        </citations>
+    </xml>
+
+    <!-- 
+        command
+    -->
+
+    <token name="@REF_FASTA@"><![CDATA[        
+        #if $reference_source.reference_source_selector == 'history':
+            ln -f -s '$reference_source.ref_file' 'reference.fa' &&
+        #else:
+            ln -f -s '$reference_source.ref_file.fields.path' 'reference.fa' &&
+        #end if
+    ]]></token>
+
+    <!--
+        input 
+    -->
+
+    <xml name="b" token_argument="-b">
+        <param argument="@ARGUMENT@" type="integer" value="100" min="1" label="Set inference batch size"/>
+    </xml>
+    <xml name="model" token_argument="-m" token_label="Select model">
+        <param argument="@ARGUMENT@" type="select" label="@LABEL@">
+            <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="r103_min_high_g360">r103_min_high_g360</option>
+            <option value="r103_prom_high_g360">r103_prom_high_g360</option>
+            <option value="r103_prom_snp_g3210">r103_prom_snp_g3210</option>
+            <option value="r103_prom_variant_g3210">r103_prom_variant_g3210</option>
+            <option value="r941_min_fast_g303">r941_min_fast_g303</option>
+            <option value="r941_min_high_g303">r941_min_high_g303</option>
+            <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_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_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>
+            <option value="r941_prom_variant_g322">r941_prom_variant_g322</option>
+        </param>
+    </xml>
+    <xml name="reference">
+        <conditional name="reference_source">
+            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
+                <option value="cached">Use a built-in genome</option>
+                <option value="history">Use a genome from history</option>
+            </param>
+            <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" />
+                    </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" />
+            </when>
+        </conditional>
+    </xml>
+
+    <!--
+        Help
+    -->
+
+    <token name="@WID@"><![CDATA[
+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>