--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_load.xml	Thu Feb 18 08:55:06 2016 -0500
@@ -0,0 +1,101 @@
+<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 &&
+        bgzip -c input.vcf > input.vcf.gz &&
+        tabix -p vcf input.vcf.gz &&
+
+        gemini
+            #if $annotation_databases:
+                --annotation-dir "${annotation_databases.fields.path}"
+            #end if
+            @BINARY@
+            -v input.vcf.gz
+            #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
+            $infostring
+            --cores \${GALAXY_SLOTS:-4}
+
+            "${ 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="tabular" 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-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)"/>
+
+        <param name="infostring" type="boolean" truevalue="--save-info-string" falsevalue="" checked="False"
+            label="Load INFO string from VCF file"  help="(--save-info-string)"/>
+    </inputs>
+    <outputs>
+        <data name="outfile" format="gemini.sqlite" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="infile" value="gemini_load_input.vcf" ftype="vcf" />
+            <param name="skip_gene_tables" value="True" />
+            <param name="skip_gerp_bp" value="True" />
+            <param name="skip_cadd" value="True" />
+            <param name="no_genotypes" value="True" />
+            <output name="outfile" file="gemini_load_result.db" compare="sim_size" delta="1000"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+**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.
+
+    ]]></help>
+    <expand macro="citations"/>
+</tool>