Add pixy wrapper

tools/pixy/.shed.yml

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+categories:
+- Statistics
+- Population Genetics
+- Genomics
+description: Unbiased estimates of pi, dxy, fst, Watterson's theta, and Tajima's D from VCFs with invariant sites
+homepage_url: https://github.com/ksamuk/pixy
+long_description: |
+  pixy addresses a fundamental limitation in population genetics: when invariant sites
+  are excluded from a VCF, estimates of pi, dxy, and fst become biased because the
+  denominator (total callable sites) is unknown. pixy requires all-sites VCFs (or a
+  variants-only VCF + wisp BED for callable sites) to produce unbiased estimates.
+name: pixy
+owner: iuc
+remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/pixy
+type: unrestricted

tools/pixy/macros.xml

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+<macros>
+    <token name="@TOOL_VERSION@">2.2.3</token>
+    <token name="@VERSION_SUFFIX@">0</token>
+    <token name="@PROFILE@">25.0</token>
+    <xml name="requirements">
+        <requirements>
+            <requirement type="package" version="@TOOL_VERSION@">pixy</requirement>
+            <requirement type="package" version="1.21">htslib</requirement>
+        </requirements>
+    </xml>
+    <xml name="version_command">
+        <version_command><![CDATA[pixy --version 2>&1 | grep -o 'version [0-9.]*' | awk '{print $2}']]></version_command>
+    </xml>
+    <xml name="citations">
+        <citations>
+            <citation type="doi">10.1111/1755-0998.13326</citation>
+        </citations>
+    </xml>
+</macros>

tools/pixy/test-data/diploid_populations.txt

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+ERS224670	BFS
+ERS224248	BFS
+ERS224089	BFS
+ERS224283	BFS
+ERS224300	KES
+ERS224168	KES
+ERS224314	KES
+ERS224235	KES

tools/pixy/test-data/haploid_populations.txt

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+tsk_1	A
+tsk_2	A
+tsk_3	A
+tsk_4	A
+tsk_5	A
+tsk_6	A
+tsk_7	A
+tsk_8	A
+tsk_9	A
+tsk_10	A
+tsk_11	B
+tsk_12	B
+tsk_13	B
+tsk_14	B
+tsk_15	B
+tsk_16	B
+tsk_17	B
+tsk_18	B
+tsk_19	B
+tsk_20	B

tools/pixy/test-data/haploid_windows.bed

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+chr1	1	300
+chr2	1	300