# HG changeset patch
# User Lance Parsons <lparsons@princeton.edu>
# Date 1314218668 14400
# Node ID 5b40b93ebae3fa83741fd3ea28dadaee6d8a1fe4
# Parent  3112c78841c5d3d409a95967e779cb485260a71d
Added advanced settings

diff -r 3112c78841c5 -r 5b40b93ebae3 bam_to_bigwig.xml
--- a/bam_to_bigwig.xml	Wed Aug 24 14:45:29 2011 -0400
+++ b/bam_to_bigwig.xml	Wed Aug 24 16:44:28 2011 -0400
@@ -8,7 +8,11 @@
 		genomeCoverageBed -ibam $align -bg $split -g 
 		`awk '($0 !~ /^#.*/) &amp;&amp; ($2 == "$align.dbkey") {print $3}' ${GALAXY_DATA_INDEX_DIR}/sam_fa_indices.loc`.fai
 		> tmp.bedgraph;
-		bedGraphToBigWig tmp.bedgraph 
+		bedGraphToBigWig 
+		#if $settings.settingsType == "full":
+     			-blockSize=${settings.blockSize} -itemsPerSlot=${settings.itemsPerSlot} ${settings.unc}
+    		#end if
+		tmp.bedgraph 
 		`awk '($0 !~ /^#.*/) &amp;&amp; ($2 == "$align.dbkey") {print $3}' ${GALAXY_DATA_INDEX_DIR}/sam_fa_indices.loc`.fai
 	       	$out;
 	</command>
@@ -18,6 +22,19 @@
 			<validator type="dataset_metadata_in_file" filename="sam_fa_indices.loc" metadata_name="dbkey" metadata_column="1" message="Sequences are not currently available for the specified build." line_startswith="index" />
 		</param>
 		<param name="split" type="boolean" value="false" label="Separate split reads" help="Do not use gaps when computing coverage. This is recommended for RNA-Seq where reads are mapped across long splice junctions. Uses the CIGAR &quot;N&quot; and &quot;D&quot; operations to infer the blocks for computing coverage." truevalue="-split" falsevalue="" /> 
+		 <conditional name="settings">
+      <param name="settingsType" type="select" label="Converter settings to use" help="Default settings should usually be used.">
+        <option value="preset">Default</option>
+        <option value="full">Full parameter list</option>
+      </param>
+      <when value="preset" />
+      <when value="full">
+        <param name="blockSize" size="4" type="integer" value="256" label="Items to bundle in r-tree" help="Default is 256 (blockSize)" />
+        <param name="itemsPerSlot" size="4" type="integer" value="1024" label="Data points bundled at lowest level" help="Default is 1024 (itemsPerSlot)" />
+        <param name="unc" type="boolean" truevalue="-unc" falsevalue="" checked="False" label="Do not use compression" help="(unc)"/>
+      </when>
+    </conditional>
+ 
 	</inputs>
 	<outputs>
 		<data format="bigwig" name="out" />