--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanopolish_extract.xml	Wed Sep 06 12:15:45 2017 -0400
@@ -0,0 +1,86 @@
+<tool id="nanopolish_extract" name="Nanopolish::extract" version="0.7.2">
+
+    <description>FAST5 to FASTQ/A extraction</description>
+
+    <!-- ***************************************************************** -->
+   
+    <!--
+    <requirements>
+        <requirement type="package" version="0.7.2">nanopolish</requirement>
+    </requirements>
+    -->
+
+    <!-- ***************************************************************** -->
+
+    <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>
+
+    <!-- ***************************************************************** -->
+
+    <command detect_errors="aggressive">
+    <![CDATA[
+
+    python3 $__tool_directory__/nanopolish_extract.py $input $output \${GALAXY_SLOTS:-1}
+
+    ]]>
+    </command>
+
+    <!-- ***************************************************************** -->
+
+    <inputs>
+
+        <param name="input" type="data" format="fast5_archive" label="Input reads" />
+        <param name="out_format" type="select" label="Output format">
+            <option value="fastq" selected="true">fastq</option>
+            <option value="fasta">fasta</option>
+        </param>
+
+    </inputs>
+
+    <!-- ***************************************************************** -->
+
+    <outputs>
+
+        <data name="output" format="fastqsanger" label="${tool.name} on ${on_string}">
+            <change_format>
+                <when input="out_format" value="fasta" format="fasta" />
+            </change_format>
+        </data>
+
+    </outputs>
+
+    <!-- ***************************************************************** -->
+
+    <tests>
+        <test>
+            <param name="input" value="test_data.fast5.tar.gz" ftype="fast5_archive" />
+            <output name="output" file="test_data.fastq" compare="sim_size" delta="0"/>
+        </test>
+    </tests>
+
+    <!-- ***************************************************************** -->
+
+    <help>
+    <![CDATA[
+
+**Description**
+
+Nanopolish is a software package for signal-level analysis of Oxford Nanopore
+sequencing data. Nanopolish can calculate an improved consensus sequence for a
+draft genome assembly, detect base modifications, call SNPs and indels with
+respect to a reference genome and more.
+
+The Galaxy wrapper has modified nanopolish to take a gzip tarball of FAST5 reads
+as input, such as can be produced by `poretools combine`, and always outputs a
+single FASTQ file.
+
+This is the `extract` module.
+
+    ]]>
+    </help>
+
+    <!-- ***************************************************************** -->
+    
+    <citations>
+    </citations>
+
+</tool>