changeset 5:feeeee14729e

Deleted selected files

--- a/evaluate_population_numbers.xml	Thu Apr 05 15:09:12 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,54 +0,0 @@
-<tool id="gd_evaluate_population_numbers" name="Evaluate" version="1.0.0">
-  <description>possible numbers of populations</description>
-
-  <command interpreter="bash">
-    evaluate_population_numbers.bash "${input.extra_files_path}/admix.ped" "$output" "$max_populations"
-  </command>
-
-  <inputs>
-    <param name="input" type="data" format="wped" label="Dataset" />
-    <param name="max_populations" type="integer" min="1" value="5" label="Maximum number of populations" />
-  </inputs>
-
-  <outputs>
-    <data name="output" format="txt" />
-  </outputs>
-
-  <tests>
-    <test>
-      <param name='input' value='fake' ftype='wped' >
-        <metadata name='base_name' value='admix' />
-        <composite_data value='genome_diversity/test_out/prepare_population_structure/prepare_population_structure.html' />
-        <composite_data value='genome_diversity/test_out/prepare_population_structure/admix.ped' />
-        <composite_data value='genome_diversity/test_out/prepare_population_structure/admix.map' />
-        <edit_attributes type='name' value='fake' />
-      </param>
-      <param name='max_populations' value='2' />
-
-      <output name="output" file="genome_diversity/test_out/evaluate_population_numbers/evaluate_population_numbers.txt" />
-    </test>
-  </tests>
-
-  <help>
-**What it does**
-
-The users selects a set of data generated by the Galaxy tool to "prepare
-to look for population structure".  For all possible numbers K of ancestral
-populations, from 1 up to a user-specified maximum, this tool produces values
-that indicate how well the data can be explained as genotypes from individuals
-derived from K ancestral populations.  These values are computed by a 5-fold
-cross-validation procedure, so that a good choice for K will exhibit a low
-cross-validation error compared with other potential settings for K.
-
-**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. Admixture is called with the "--cv"
-flag to produce these values.
-  </help>
-</tool>