--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_comp_hets.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,61 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Identifying potential compound heterozygotes</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">comp_hets</token>
+    </macros>
+    <command>
+<![CDATA[
+        gemini @BINARY@
+
+            #if $report.report_selector != 'all':
+                --columns "${report.columns}"
+            #end if
+
+            #if $filter.filter_selector == 'yes':
+                --filter "${filter.filter}"
+            #end if
+            $only_affected
+            $ignore_phasing
+
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+        <expand macro="add_header_column" />
+        <expand macro="column_filter" />
+        <param name="only_affected" type="boolean" truevalue="--only-affected" falsevalue="" checked="False" 
+            label="Report solely those compund heterozygotes impacted a sample labeled as affected" help="(--only-affected)"/>
+        <param name="ignore_phasing" type="boolean" truevalue="--ignore-phasing" falsevalue="" checked="False" 
+            label="Ignore phasing when screening for compound hets" help="Candidates are inherently putative. (--ignore-phasing)"/>
+        <expand macro="filter" />
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+Many recessive disorders are caused by compound heterozygotes. Unlike canonical recessive sites where the same recessive allele is 
+inherited from both parents at the _same_ site in the gene, compound heterozygotes occur when the individual’s phenotype is caused 
+by two heterozygous recessive alleles at _different_ sites in a particular gene.
+
+So basically, we are looking for two (typically loss-of-function (LoF)) heterozygous variants impacting the same gene at different loci. 
+The complicating factor is that this is _recessive_ and as such, we must also require that the consequential alleles at each heterozygous 
+site were inherited on different chromosomes (one from each parent). As such, in order to use this tool, we require that all variants are phased. 
+Once this has been done, the comp_hets tool will provide a report of candidate compound heterozygotes for each sample/gene.
+
+
+@CITATION@
+    </help>
+    <expand macro="citations"/>
+</tool>