--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gemini_query.xml	Mon Aug 25 17:15:54 2014 -0400
@@ -0,0 +1,110 @@
+<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
+    <description>Querying the GEMINI database</description>
+    <expand macro="requirements" />
+    <expand macro="version_command" />
+    <macros>
+        <import>gemini_macros.xml</import>
+        <token name="@BINARY@">query</token>
+    </macros>
+    <command>
+<![CDATA[
+        gemini @BINARY@
+
+            --in "${in}"
+
+            #if $gt_filter.strip():
+                --gt-filter "${gt_filter}"
+            #end if
+
+            #if $sample_filter.strip():
+                --sample-filter "${sample_filter}"
+            #end if
+
+            $show_samples
+            $show_families
+            $family_wise
+            $header
+            $dgidb
+            #if $region.strip():
+                --region "${region}"
+            #end if
+            #if int($min_kindreds) > 0:
+                --min-kindreds $min_kindreds
+            #end if
+            ##--format FORMAT       Format of output (JSON, TPED or default) # we will take default for the time being
+            ##   --sample-delim STRING The delimiter to be used with the --show-samples option.
+
+            #if $q.strip():
+                -q "${q}"
+            #end if
+
+            "${ infile }"
+            > "${ outfile }"
+]]>
+    </command>
+                <!--
+            ##TODO:
+              - -carrier-summary-by-phenotype CARRIER_SUMMARY
+                        Output columns of counts of carriers and non-carriers
+                        stratified by the given sample phenotype column-->
+    <expand macro="stdio" />
+    <inputs>
+        <param name="infile" type="data" format="sqlite" label="GEMINI database" />
+
+        <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)">
+            <expand macro="sanitize_query" />
+        </param>
+        <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)">
+            <expand macro="sanitize_query" />
+        </param>
+        <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table" help="(--sample-filter)">
+            <expand macro="sanitize_query" />
+        </param>
+
+        <param name="show_samples" type="boolean" truevalue="--show-samples" falsevalue="" checked="False" 
+            label="Add a column of all sample names with a variant to each variant" help="(--show-samples)"/>
+
+        <param name="show_families" type="boolean" truevalue="--show-families" falsevalue="" checked="False" 
+            label="Add a column listing all of the families with a variant to each variant" help="(--show-families)"/>
+
+        <param name="family_wise" type="boolean" truevalue="--family-wise" falsevalue="" checked="False" 
+            label="Perform the sample-filter on a family-wise basis" help="(--family-wise)"/>
+
+        <expand macro="add_header_column" />
+
+        <!-- TODO: is there any default values set? -->
+        <param name="min_kindreds" size="4" type="integer" value="-1" lebel="Minimum number of families for a variant passing a family-wise filter to be in" help="-1 means default values (--min-kindreds)" />
+
+        <param name="dgidb" type="boolean" truevalue="--dgidb" falsevalue="" checked="False" 
+            label="Request drug-gene interaction info from DGIdb" help="(--dgidb)"/>
+
+        <param name="in" type="select" label="A variant must be in either all, none or any samples passing the sample-query filter" help="(--in)">
+            <option value="all">Return a variant if all samples matching the query have the variant. (all)</option>
+            <option value="none">Return a variant if the variant does not appear in any of the matching samples. (none)</option>
+            <option value="any">Return all of the variant which are in all of the matching samples and not in any of the non-matching samples. (any)</option>
+            <option value="only">Return a variant if the variant is only in the matching samples and not in any of the non-matching samples. (only)</option>
+        </param>
+
+        <param name="region" size="30" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/>
+
+
+    </inputs>
+    <outputs>
+        <data name="outfile" format="tabular" label="${tool.name} on ${on_string}" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+The real power in the GEMINI framework lies in the fact that all of your genetic variants have been stored in a convenient database in the context of a wealth of genome annotations that facilitate variant interpretation. 
+The expressive power of SQL allows one to pose intricate questions of one’s variation data. This tool offers you an easy way to query your variants!
+
+http://gemini.readthedocs.org/en/latest/content/querying.html
+
+@CITATION@
+    </help>
+    <expand macro="citations"/>
+</tool>