--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanopolish_index.xml	Mon Feb 12 00:58:10 2018 -0500
@@ -0,0 +1,82 @@
+<tool id="nanopolish_index" name="Nanopolish::index" version="0.8.5">
+
+    <description>Index FASTQ reads in FAST5 file</description>
+
+    <!-- ***************************************************************** -->
+   
+    <requirements>
+        <requirement type="package" version="0.8.5">nanopolish</requirement>
+    </requirements>
+
+    <!-- ***************************************************************** -->
+
+    <version_command>nanopolish --version | perl -wnE'print "$1\n" for /^nanopolish version (.+)$/mg'</version_command>
+
+    <!-- ***************************************************************** -->
+
+    <command detect_errors="aggressive">
+    <![CDATA[
+
+    perl $__tool_directory__/nanopolish_index.pl
+
+        --reads $input_reads
+        --fast5 $input_fast5
+        --out   $out_index
+
+    ]]>
+    </command>
+
+    <!-- ***************************************************************** -->
+
+    <inputs>
+
+        <param name="input_reads" type="data" format="fasta,fastq" label="Input reads (FASTA/Q)" />
+        <param name="input_fast5" type="data" format="fast5.tar" label="Input reads (FAST5)" />
+
+    </inputs>
+
+    <!-- ***************************************************************** -->
+
+    <outputs>
+
+        <data name="out_index" format="tar" label="${tool.name} on ${on_string}" />
+
+    </outputs>
+
+    <!-- ***************************************************************** -->
+
+    <tests>
+        <test>
+            <param name="input_reads" value="called.fa" ftype="fasta" />
+            <param name="input_fast5" value="test.fast5.tar.gz" ftype="fast5.tar.gz" />
+            <output name="out_index" file="index.tar" compare="sim_size" delta="100"/>
+        </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 `index` module.
+
+    ]]>
+    </help>
+
+    <!-- ***************************************************************** -->
+    
+    <citations>
+    </citations>
+
+</tool>