--- a/gemini_comp_hets.xml	Fri Oct 16 13:55:09 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,60 +0,0 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
-    <description>Identifying potential compound heterozygotes</description>
-    <macros>
-        <import>gemini_macros.xml</import>
-        <token name="@BINARY@">comp_hets</token>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <command>
-<![CDATA[
-        gemini @BINARY@
-
-            #if $report.report_selector != 'all':
-                --columns "${report.columns}"
-            #end if
-
-            @CMDLN_SQL_FILTER_FILTER_OPTION@
-
-            $only_affected
-            $ignore_phasing
-
-            "${ infile }"
-            > "${ outfile }"
-]]>
-    </command>
-    <inputs>
-        <expand macro="infile" />
-        <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" />
-    </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>