--- a/gemini_query.xml	Fri Oct 16 13:55:09 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,110 +0,0 @@
-<tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
-    <description>Querying the GEMINI database</description>
-    <macros>
-        <import>gemini_macros.xml</import>
-        <token name="@BINARY@">query</token>
-    </macros>
-    <expand macro="requirements" />
-    <expand macro="stdio" />
-    <expand macro="version_command" />
-    <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-->
-    <inputs>
-        <expand macro="infile" />
-
-        <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" type="integer" value="-1" label="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" type="text" value="" label="Restrict query to this region" help="e.g. chr1:10-20 (--region)"/>
-
-
-    </inputs>
-    <outputs>
-        <data name="outfile" format="tabular" />
-    </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>