--- a/gemini_query.xml	Mon Aug 11 07:45:22 2014 -0400
+++ b/gemini_query.xml	Sun Aug 24 17:49:00 2014 -0400
@@ -1,5 +1,5 @@
 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
-    <description></description>
+    <description>Querying the GEMINI database</description>
     <expand macro="requirements" />
     <expand macro="version_command" />
     <macros>
@@ -10,9 +10,7 @@
 <![CDATA[
         gemini @BINARY@
 
-            #if $q.strip():
-                -q "${q}"
-            #end if
+            --in "${in}"
 
             #if $gt_filter.strip():
                 --gt-filter "${gt_filter}"
@@ -27,7 +25,6 @@
             $family_wise
             $header
             $dgidb
-            --in $in
             #if $region.strip():
                 --region "${region}"
             #end if
@@ -37,8 +34,9 @@
             ##--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 }"
@@ -53,10 +51,9 @@
     <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"/>
-        <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values"/>
-        <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table"/>
-        <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table"/>
+        <param name="q" type="text" area="True" size="5x50" label="The query to be issued to the database" help="(-q)"/>
+        <param name="gt_filter" type="text" area="True" size="5x50" label="Restrictions to apply to genotype values" help="(--gt-filer)"/>
+        <param name="sample_filter" type="text" area="True" size="5x50" label="SQL filter to use to filter the sample table" help="(--sample-filter)"/>
 
         <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)"/>
@@ -76,10 +73,10 @@
             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">all</option>
-            <option value="none">none</option>
-            <option value="any">any</option>
-            <option value="only">only</option>
+            <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)"/>