--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/nanopolish_variants.xml	Wed Sep 06 12:15:45 2017 -0400
@@ -0,0 +1,100 @@
+<tool id="nanopolish_variants" name="Nanopolish::variants" version="0.7.2">
+
+    <description>Re-call consensus and variants from raw signal</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[
+
+    ln -s $input_bam 'input.bam'  &&
+    ln -s $input_bam.metadata.bam_index input.bai &&
+
+    perl $__tool_directory__/nanopolish_variants.pl variants
+
+        --reads     $input_reads
+        --bam       input.bam
+        --genome    $input_ref
+        --consensus $out_consensus
+        --outfile   $out_variants
+        --threads \${GALAXY_SLOTS:-1}
+        --max-round $max_rounds
+        --max-haplotypes $max_haplotypes
+        --min-candidate-depth $min_candidate_depth
+        --min-candidate-frequency $min_candidate_frequency
+        --fast5 $input_fast5
+        $fix_homopolymers
+        $calculate_all_support
+
+    ]]>
+    </command>
+
+    <!-- ***************************************************************** -->
+
+    <inputs>
+
+        <param name="input_reads" type="data" format="fasta" label="Input reads (FASTA)" />
+        <param name="input_fast5" type="data" format="fast5_archive" label="Input reads (FAST5)" />
+        <param name="input_bam"   type="data" format="bam"   label="Alignment" />
+        <param name="input_ref"   type="data" format="fasta" label="Reference" />
+        <param name="min_candidate_frequency" type="float" value="0.2" size="5" label="Minimum candidate frequency" />
+        <param name="min_candidate_depth" type="integer" min="1" value="20" size="5" label="Minimum candidate depth" />
+        <param name="max_haplotypes" type="integer" min="0" value="1000" size="5" label="Maximum haplotype combinations" />
+        <param name="max_rounds" type="integer" min="0" value="50" size="5" label="Maximum iterations" />
+        <param name="fix_homopolymers" type="boolean" checked="false" truevalue="--fix-homopolymers" falsevalue="" label="Fix homopolymers" />
+        <param name="calculate_all_support" type="boolean" checked="false" truevalue="--calculate-all-support" falsevalue="" label="Calculate support for all four bases" /> 
+    </inputs>
+
+    <!-- ***************************************************************** -->
+
+    <outputs>
+
+        <data name="out_variants" format="vcf" label="${tool.name} on ${on_string} (variants)" />
+        <data name="out_consensus" format="fasta" label="${tool.name} on ${on_string} (consensus)" />
+
+    </outputs>
+
+    <!-- ***************************************************************** -->
+
+    <tests>
+    </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>