--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp-dists.xml	Sat Oct 19 05:08:45 2019 -0400
@@ -0,0 +1,83 @@
+<tool id="snp_dists" name="SNP distance matrix" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
+    <macros>
+        <token name="@TOOL_VERSION@">0.6.3</token>
+    </macros>
+    <description>Compute distance in SNPs between all sequences in a FASTA file</description>
+    <requirements>
+        <requirement type="package" version="@TOOL_VERSION@">snp-dists</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+        snp-dists -q 
+            $a
+            $k
+            $b
+            '$input' > '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" type="data" format="fasta,fasta.gz" label="FASTA multiple sequence alignment" 
+            help="Provide a multiple sequence alignment containing sequences of equal length" />
+        <param argument="-a" type="boolean" truevalue="-a" falsevalue="" label="Count all differences, not just ACTG" />
+        <param argument="-k" type="boolean" truevalue="-k" falsevalue="" label="Keep case, don't uppercase all letters" />
+        <param argument="-b" type="boolean" truevalue="-b" falsevalue="" label="Blank top left corner cell" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="input" ftype="fasta" value="input1.fasta" />
+            <output name="output" value="output_default1.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input" ftype="fasta" value="input1.fasta" />
+            <param name="a" value="True" />
+            <output name="output" value="output_all_diffs1.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input" ftype="fasta" value="input1.fasta" />
+            <param name="k" value="True" />
+            <output name="output" value="output_keep_case1.tabular" ftype="tabular" />
+        </test>
+        <test>
+            <param name="input" ftype="fasta" value="input1.fasta" />
+            <param name="b" value="True" />
+            <output name="output" value="output_blank_cell1.tabular" ftype="tabular" />
+        </test>
+    </tests>
+    <help><![CDATA[
+    **snp-dists**
+
+    This tool computes a SNP distance matrix from a multiple sequence alignment (MSA) of
+    sequences (all of the same length). Such distance matrices are often used as in
+    studies of disease outbreaks.
+
+    The output is a tabular file, for example this matrix describing four M. tuberculosis isolates
+    and their relationship to the inferred ancestral reference sequence:
+
+=============== ======= =========   =========   =========   =========
+snp-dists 0.6.3	MTB_anc	ERR550641   ERR550671   ERR550691   ERR550703
+--------------- ------- ---------   ---------   ---------   ---------
+MTB_anc	        0       746         726         772         749
+--------------- ------- ---------   ---------   ---------   ---------
+ERR550641       746     0           26          44          13
+--------------- ------- ---------   ---------   ---------   ---------
+ERR550671       726     26          0           64          29
+--------------- ------- ---------   ---------   ---------   ---------
+ERR550691       772     44          64          0           39
+--------------- ------- ---------   ---------   ---------   ---------
+ERR550703       749     13          29          39          0
+=============== ======= =========   =========   =========   =========
+
+    ]]></help>
+    <citations>
+        <citation type="bibtex">
+@misc{githubsnp-dists,
+  author = {Seemann, Torsten},
+  year = {2019},
+  title = {snp-dists},
+  publisher = {GitHub},
+  journal = {GitHub repository},
+  url = {https://github.com/tseemann/snp-dists},
+}</citation>
+    </citations>
+</tool>