--- a/macros.xml	Tue Nov 04 01:45:04 2014 -0500
+++ b/macros.xml	Thu Jan 08 14:25:51 2015 -0500
@@ -1,11 +1,12 @@
 <macros>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="2.19.1">bedtools</requirement>
+            <requirement type="package" version="2.22">bedtools</requirement>
+            <yield/>
         </requirements>
         <version_command>bedtools --version</version_command>
     </xml>
-    <token name="@WRAPPER_VERSION@">2.19</token>
+    <token name="@WRAPPER_VERSION@">2.22</token>
     <xml name="stdio">
         <stdio>
             <!-- Anything other than zero is an error -->
@@ -16,9 +17,13 @@
             <regex match="Exception:" />
         </stdio>
     </xml>
-
+    <xml name="reciprocal">
+        <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue=""
+            label="Require that the fraction of overlap be reciprocal for A and B"
+            help="In other words, if -f is 0.90 and -r is used, this requires that B overlap at least 90% of A and that A also overlaps at least 90% of B. (-r)" />
+    </xml>
     <xml name="overlap">
-        <param name="overlap" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" />
+        <param name="overlap" type="float" value="0.000000001" label="Minimum overlap required as a fraction of A" help="Default is 1E-9, i.e. 1bp. (-f)"/>
     </xml>
     <xml name="strand2">
         <param name="strand" type="select" label="Calculation based on strandedness?">
@@ -29,19 +34,24 @@
     </xml>
     <xml name="seed">
         <conditional name="seed">
-            <param name="choose" type="boolean" label="Choose Seed?" selected="False" truevalue="True" falsevalue="False" />
+            <param name="seed_choose" type="select" label="Choose Seed?" help="(-seed)">
+                <option value="False" selected="True">Random Shuffling</option>
+                <option value="True">Choose fixed seed</option>
+            </param>
             <when value="True">
                 <param name="seed" type="integer" value="12345" label="Enter Seed" />
             </when>
+            <when value="False" />
         </conditional>
     </xml>
     <xml name="split">
-        <param name="split" type="boolean" checked="true" truevalue="-split" falsevalue="" 
+        <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" 
             label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." 
-            help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
+            help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data. (-split)" />
     </xml>
     <xml name="genome">
-        <param format="bed,vcf,gff,gff3" name="genome" type="data" label="Genome file" />
+        <param format="tabular" name="genome" type="data" label="Genome file" />
+        <!--TODO: make use of: ${chromInfo} -->
     </xml>
     <xml name="addition">
         <conditional name="addition">
@@ -50,30 +60,61 @@
                 <option value="lr">Increase by Start Coordinate and End Coordinate</option>
             </param>
             <when value="b">
-                <param name="b" label="Give Value" type="integer" value="0"  />
+                <param name="b" value="1" label="Number of base pairs" type="integer" />
             </when>
             <when value="lr">
-                <param name="l" label="The number of base pairs to subtract from the start coordinate" type="integer" value="0" />
-                <param name="r" label="The number of base pairs to add to the end coordinate" type="integer" value="0" />
+                <param name="l" type="integer" value="0" label="The number of base pairs to subtract from the start coordinate" />
+                <param name="r" type="integer" value="0" label="The number of base pairs to add to the end coordinate" />
             </when>
         </conditional>
     </xml>
+    <xml name="print_header">
+        <param name="header" type="boolean" checked="False" truevalue="-header" falsevalue=""
+            label="Print the header from the A file prior to results" help="(-header)" />
+    </xml>
+    <!-- TODO this is currently not used, but we should make use of it -->
+    <xml name="genome_validator">
+        <validator type="unspecified_build" />
+        <validator type="dataset_metadata_in_data_table" table_name="fasta_indexes" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." />
+    </xml>
+
+    <!-- ToDo column_picker -->
+    <xml name="choose_columns">
+        <param name="cols" type="text" value=""
+            label="Specify the column(s) (comma separated) that should be summarized"
+            help="(-c)">
+            <sanitizer invalid_char="">
+                <valid initial="string.digits"><add value=","/></valid>
+            </sanitizer>
+        </param>
+    </xml>
+
+    <xml name="choose_operations">
+        <param name="operation" type="select" label="Specify the operation">
+            <yield />
+        </param>
+    </xml>
+
     <xml name="math_options">
-            <option value="min">Min - numeric only</option>
-            <option value="max">Max - numeric only</option>
-             <option value="mean">Mean - numeric only</option>
-            <option value="median">Median - numeric only</option>
-            <option value="mode">Mode - numeric only</option>
-            <option value="antimode">Antimode - numeric only</option>
-            <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
-       </xml>
+        <option value="sum" selected="True">Sum - numeric only</option>
+        <option value="min">Min - numeric only</option>
+        <option value="max">Max - numeric only</option>
+        <option value="absmin">AbsMin - numeric only</option>
+        <option value="absmax">AbsMax - numeric only</option>
+        <option value="mean">Mean - numeric only</option>
+        <option value="median">Median - numeric only</option>
+        <option value="mode">Mode - numeric only</option>
+        <option value="antimode">Antimode - numeric only</option>
+        <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
+    </xml>
     <xml name="additional_math_options">
-            <option value="count">Count - numeric or text</option>
-            <option value="count_disctinct">Count Distinct - numeric or text</option>
-            <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
-            <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
+        <option value="count">Count - numeric or text</option>
+        <option value="count_disctinct">Count Distinct - numeric or text</option>
+        <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
+        <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
     </xml>
     <token name="@REFERENCES@">
+<![CDATA[
 ------
 
 This tool is part of the `bedtools package`_ from the `Quinlan laboratory`_.
@@ -81,10 +122,18 @@
 .. _bedtools package: https://github.com/arq5x/bedtools2
 .. _Quinlan laboratory: http://cphg.virginia.edu/quinlan/
 
+
+**Citation**
+
+If you use this tool in Galaxy, please cite:
+
+Bjoern A. Gruening (2014), `Galaxy wrapper <https://github.com/bgruening/galaxytools>`_
+]]>
     </token>
     <xml name="citations">
         <citations>
             <citation type="doi">10.1093/bioinformatics/btq033</citation>
+            <yield />
         </citations>
     </xml>
 </macros>