--- a/gemini_load.xml	Fri Oct 16 13:55:09 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,91 +0,0 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
-    <description>Loading a VCF file into GEMINI</description>
-    <macros>
-        <import>gemini_macros.xml</import>
-        <token name="@BINARY@">load</token>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <command>
-<![CDATA[
-        ln -s "${ infile }" input.vcf &&
-
-        gemini
-            --annotation-dir ${annotation_databases.fields.path}
-            @BINARY@
-            -v input.vcf
-            #if str( $annotation_type ) != "None":
-                -t $annotation_type
-            #end if
-
-            #if $ped:
-                -p $ped
-            #end if
-
-            $skip_gerp_bp
-            $skip_cadd
-            $skip_gene_tables
-            $no_load_genotypes
-            $no_genotypes
-            $passonly
-            --cores \${GALAXY_SLOTS:-4}
-
-            "${ outfile }"
-]]>
-    </command>
-    <inputs>
-        <param name="infile" type="data" format="vcf" label="VCF file to be loaded in the GEMINI database" help="Only build 37 (aka hg19) of the human genome is supported.">
-            <options>
-                <filter type="add_value" value="hg19" />
-                <filter type="add_value" value="Homo_sapiens_nuHg19_mtrCRS" />
-                <filter type="add_value" value="hg_g1k_v37" />
-            </options>
-        </param>
-
-        <param name="annotation_type" type="select" label="The annotations to be used with the input vcf" help="(-t)">
-            <option value="None">None (not recommended)</option>
-            <option value="snpEff" selected="True">snpEff annotated VCF file</option>
-            <option value="VEP">VEP annotated VCF file</option>
-        </param>
-        <param name="ped" type="data" format="tablar" optional="True" label="Sample information file in PED+ format" help="(-p)" />
-        <expand macro="annotation_dir" />
-
-        <param name="skip_gerp_bp" type="boolean" truevalue="--skip-gerp-bp" falsevalue="" checked="False"
-            label="Do not load GERP scores at base pair resolution" help="(--skip-gerp-bp)"/>
-
-        <param name="skip_cadd" type="boolean" truevalue="--skip-cadd" falsevalue="" checked="False"
-            label="Do not load CADD scores" help="(--skip-cadd)"/>
-
-        <param name="skip_gene_tables" type="boolean" truevalue="--skip-gene-tables" falsevalue="" checked="False"
-            label="Do not load gene tables" help="(--skip-gene-tables)"/>
-
-        <param name="no_load_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False"
-            label="Genotypes exist in the file, but should not be stored" help="(--no-load-genotypes)"/>
-
-        <param name="no_genotypes" type="boolean" truevalue="--no-load-genotypes" falsevalue="" checked="False"
-            label="There are no genotypes in the file" help="e.g. some 1000G VCFs (--no-genotypes)"/>
-
-        <param name="passonly" type="boolean" truevalue="--passonly" falsevalue="" checked="False"
-            label="Keep only variants that pass all filters" help="e.g. some 1000G VCFs (--passonly)"/>
-
-    </inputs>
-    <outputs>
-        <data name="outfile" format="gemini.sqlite" />
-    </outputs>
-    <tests>
-        <test>
-        </test>
-    </tests>
-    <help>
-**What it does**
-
-Before we can use GEMINI to explore genetic variation, we must first load our VCF file into the GEMINI database framework.
-We expect you to have first annotated the functional consequence of each variant in your VCF using either VEP or snpEff.
-
-http://gemini.readthedocs.org/en/latest/content/loading.html
-
-@CITATION@
-    </help>
-    <expand macro="citations"/>
-</tool>