diff population_structure.xml @ 14:8ae67e9fb6ff

Uploaded Miller Lab Devshed version a51c894f5bed again [possible toolshed.g2 bug]

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/population_structure.xml	Fri Sep 28 11:35:56 2012 -0400
@@ -0,0 +1,72 @@
+<tool id="gd_population_structure" name="Ancestry" version="1.0.0">
+  <description>: Characterize ancestries w.r.t. inferred ancestral populations</description>
+
+  <command interpreter="python">
+    population_structure.py "$input" "${input.extra_files_path}/admix.ped" "$output" "$output.files_path" "$populations"
+  </command>
+
+  <inputs>
+    <param name="input" type="data" format="gd_ped" label="Dataset" />
+    <param name="populations" type="integer" min="1" value="2" label="Number of populations" />
+  </inputs>
+
+  <outputs>
+    <data name="output" format="html" />
+  </outputs>
+
+  <!--
+  <tests>
+    <test>
+      <param name="input" value="fake" ftype="gd_ped" >
+        <metadata name="base_name" value="admix" />
+        <composite_data value="test_out/prepare_population_structure/prepare_population_structure.html" />
+        <composite_data value="test_out/prepare_population_structure/admix.ped" />
+        <composite_data value="test_out/prepare_population_structure/admix.map" />
+        <edit_attributes type="name" value="fake" />
+      </param>
+      <param name="populations" value="2" />
+
+      <output name="output" file="test_out/population_structure/population_structure.html" ftype="html" compare="diff" lines_diff="2">
+        <extra_files type="file" name="numeric.txt" value="test_out/population_structure/numeric.txt" />
+        <extra_files type="file" name="graphical.pdf" value="test_out/population_structure/graphical.pdf" compare="sim_size" delta="1000" />
+      </output>
+    </test>
+  </tests>
+  -->
+
+
+  <help>
+
+**Dataset formats**
+
+The input dataset is in gd_ped_ format.
+The output dataset is a composite dataset containing a graph and text.
+(`Dataset missing?`_)
+
+.. _gd_ped: ./static/formatHelp.html#gd_ped
+.. _Dataset missing?: ./static/formatHelp.html
+
+-----
+
+**What it does**
+
+The user selects a gd_ped dataset generated by the Prepare Input tool,
+and specifies a number, K, of ancestral
+populations.  The tool estimates the proportion of each individual's ancestry
+coming from each ancestral population.  The proportions are shown both as
+numbers and graphically.
+
+-----
+
+**Acknowledgments**
+
+We use the program "Admixture", downloaded from
+
+http://www.genetics.ucla.edu/software/admixture/
+
+and described in the paper "Fast model-based estimation of ancestry in
+unrelated individuals" by David H. Alexander, John Novembre and Kenneth Lange,
+Genome Research 19 (2009), pp. 1655-1664.
+
+  </help>
+</tool>