--- a/gemini_pathways.xml	Fri Oct 16 13:55:09 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
-    <description>Map genes and variants to KEGG pathways</description>
-    <macros>
-        <import>gemini_macros.xml</import>
-        <token name="@BINARY@">pathways</token>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <command>
-<![CDATA[
-        gemini
-            --annotation-dir ${annotation_databases.fields.path}
-            @BINARY@
-            -v $ensembl
-            $lof
-            "${ infile }"
-            > "${ outfile }"
-]]>
-    </command>
-    <inputs>
-        <expand macro="infile" />
-
-        <param name="ensembl" type="integer" value="68" label="Version of ensembl genes to use"
-            help="Supported versions: 66 to 71. use versions that match the VEP/snpEff versions of the annotated vcf for correctness. For e.g VEP v2.6 and snpEff v3.1 use Ensembl 68 version of the genomes. (-v)">
-            <validator type="in_range" min="66" max="71"/>
-        </param>
-
-        <param name="lof" type="boolean" truevalue="--lof" falsevalue="" checked="False"
-            label="Report only pathways with loss-of-function variants" help="(--lof)"/>
-        <expand macro="annotation_dir" />
-    </inputs>
-    <outputs>
-        <data name="outfile" format="tabular" />
-    </outputs>
-    <tests>
-        <test>
-        </test>
-    </tests>
-    <help>
-**What it does**
-
-Mapping genes to biological pathways is useful in understanding the function/role played by a gene.
-Likewise, genes involved in common pathways is helpful in understanding heterogeneous diseases.
-We have integrated the KEGG pathway mapping for gene variants, to explain/annotate variation.
-
-This requires your VCF be annotated with either snpEff/VEP.
-
-@CITATION@
-    </help>
-    <expand macro="citations"/>
-</tool>