diff offspring_heterozygosity_pedigree.xml @ 31:a631c2f6d913

Update to Miller Lab devshed revision 3c4110ffacc3

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/offspring_heterozygosity_pedigree.xml	Fri Sep 20 13:25:27 2013 -0400
@@ -0,0 +1,81 @@
+<tool id="gd_offspring_heterozygosity_pedigree" name="Founders sequenced" version="1.0.0">
+  <description>: Offspring estimated heterozygosity from a pedigree with sequenced founders</description>
+
+  <command interpreter="python">
+    #import json
+    #import base64
+    #import zlib
+    #set $ind_names = $input.dataset.metadata.individual_names
+    #set $ind_colms = $input.dataset.metadata.individual_columns
+    #set $ind_dict = dict(zip($ind_names, $ind_colms))
+    #set $ind_json = json.dumps($ind_dict, separators=(',',':'))
+    #set $ind_comp = zlib.compress($ind_json, 9)
+    #set $ind_arg = base64.b64encode($ind_comp)
+    offspring_heterozygosity_pedigree.py '$input' '$input.ext' '$pedigree' '$ind_arg' '$founders' '$b1_input' '$b2_input' '$output'
+  </command>
+
+  <inputs>
+    <param name="input" type="data" format="gd_snp,gd_genotype" label="SNP dataset" />
+    <param name="pedigree" type="data" format="txt" label="Pedigree dataset" />
+    <param name="founders" type="data" format="gd_indivs" label="Founders dataset" />
+    <param name="b1_input" type="data" format="txt" label="First breeders dataset" />
+    <param name="b2_input" type="data" format="txt" label="Second breeders dataset" />
+  </inputs>
+
+  <outputs>
+    <data name="output" format="txt" />
+  </outputs>
+
+  <requirements>
+    <requirement type="package" version="0.1">gd_c_tools</requirement>
+  </requirements>
+
+  <!--
+  <tests>
+  </tests>
+  -->
+
+  <help>
+
+**Dataset formats**
+
+The input datasets are in gd_snp_, gd_genotype_, text_, and gd_indivs_ formats.
+The output dataset is in text_ format.
+
+.. _gd_snp: ./static/formatHelp.html#gd_snp
+.. _gd_genotype: ./static/formatHelp.html#gd_genotype
+.. _gd_indivs: ./static/formatHelp.html#gd_indivs
+.. _text: ./static/formatHelp.html#text
+
+-----
+
+**What it does**
+
+The user provides a Galaxy SNP table (gd_snp or gd_genotype format) that
+includes the founders of a pedigree, as well as two sets of individuals.
+The pedigree is specified by a text file with one row per individual,
+containing (1) the individual's name, (2) the name of one of the
+individual's parents, which must have occurred at the start of a previous
+line, and (3) the name of the individual's other parent, which occurred at
+the start of a previous line.  For a pedigree founder, both parent names
+are replaced by &quot;-&quot;.  The founders are specified by a table in
+gd_indivs format, e.g., as produced by &quot;Specify individuals&quot;
+tool.  Every founder must have genotypes supplied in the SNP table,
+and both parents need to be given as &quot;-&quot; in the pedigree.
+Conversely, every pedigree individual whose parents are &quot;-&quot;
+must be named as a founder.
+
+The user also provides two files that specify a set of names of
+individuals.  The first word on each line names an individual (one
+line per individual); any subsequent information on a line is ignored.
+The name of each individual must appear at the start of a line in the
+pedigree.
+
+For each pair of individuals, one from each specified set, the program
+computes the expected heterozygosity of any offspring of the pair,
+i.e., the probability that the offspring has distinct nucleotides at
+a randomly chosen autosomal SNP.  A SNP is ignorned if one or both
+potential parents have an ancestor with undefined genotype (designated
+as -1 in the SNP table).
+  </help>
+</tool>