# HG changeset patch
# User timpalpant
# Date 1331088946 18000
# Node ID 9266d807ca85693189a3ad332fe532f66ed5f6fd
# Parent  5a3f8b0b80f9e6ad09bea754269eff4fc5c3b228
Uploaded

diff -r 5a3f8b0b80f9 -r 9266d807ca85 galaxy-conf/._DNAPropertyCalculator.xml
Binary file galaxy-conf/._DNAPropertyCalculator.xml has changed
diff -r 5a3f8b0b80f9 -r 9266d807ca85 galaxy-conf/BaseAlignCounts.xml
--- a/galaxy-conf/BaseAlignCounts.xml	Tue Feb 28 15:39:16 2012 -0500
+++ b/galaxy-conf/BaseAlignCounts.xml	Tue Mar 06 21:55:46 2012 -0500
@@ -12,6 +12,6 @@
   <help>
     .. class:: warningmark
     
-    This tool requires sequencing reads in BAM format.
+    This tool requires sequencing reads in SAM, BAM, or Bed format.
   </help>
 </tool>
diff -r 5a3f8b0b80f9 -r 9266d807ca85 galaxy-conf/DNAPropertyCalculator.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/galaxy-conf/DNAPropertyCalculator.xml	Tue Mar 06 21:55:46 2012 -0500
@@ -0,0 +1,83 @@
+<tool id="DNAPropertyCalculator" name="Calculate sequence-specific DNA properties" version="1.0.0">
+  <description>for a genome</description>
+  <command interpreter="sh">galaxyToolRunner.sh dna.DNAPropertyCalculator -i 
+    #if $refGenomeSource.genomeSource == "history":
+      $refGenomeSource.ownFile
+    #else
+      ${refGenomeSource.index.fields.path}
+    #end if
+	$N -p $property -o $output
+  </command>
+  <inputs>
+    <conditional name="refGenomeSource">
+      <param name="genomeSource" type="select" label="Will you select a reference genome from your history or use a built-in index?" help="Built-ins were indexed using default options">
+        <option value="indexed">Use a built-in index</option>
+        <option value="history">Use one from the history</option>
+      </param>
+      <when value="indexed">
+        <param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team">
+          <options from_data_table="sam_fa_indexes">
+            <filter type="sort_by" column="1" />
+            <validator type="no_options" message="No indexes are available" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
+      </when>  <!-- history -->
+    </conditional>  <!-- refGenomeSource -->
+
+    <param name="property" type="select" label="Property to calculate">
+      <option value="ATG-density">ATG</option>
+      <option value="G-content">G</option>
+      <option value="C-content">C</option>
+      <option value="T-content">T</option>
+      <option value="A-content">A</option>
+      <option value="GC-content">GC</option>
+      <option value="AT-content">AT</option>
+      <option value="Pyrimidine-content">Pyrimidine</option>
+      <option value="Purine-content">Purine</option>
+      <option value="Bendability">Bendability</option>
+      <option value="zDNA">zDNA</option>
+      <option value="DuplexStabilityFreeEnergy">Duplex Stability Free Energy</option>
+      <option value="DuplexStabilityDisruptEnergy">Duplex Stability Disrupt Energy</option>
+      <option value="DNADenaturation">DNA Denaturation</option>
+      <option value="PropellorTwist">Propellor Twist</option>
+      <option value="BaseStacking">Base Stacking</option>
+      <option value="ProteinDeformation">Protein Deformation</option>
+      <option value="BendingStiffness">Bending Stiffness</option>
+      <option value="ProteinDNATwist">Protein DNA Twist</option>
+      <option value="bDNATwist">bDNA Twist</option>
+      <option value="APhilicity">APhilicity</option>
+      <option value="NucleosomePosition">Nucleosome Position (trinucleotide model)</option>
+      <option value="Twist">Twist</option>
+      <option value="Tilt">Tilt</option>
+      <option value="Roll">Roll</option>
+      <option value="Slide">Slide</option>
+      <option value="Rise">Rise</option>
+    </param>
+    
+    <param name="N" type="boolean" checked="true" truevalue="-n" falsevalue="" label="Output normalized values" />
+  </inputs>
+  <outputs>
+      <data format="wig" name="output" label="Calculate ${property.value_label}">
+        <actions>
+          <conditional name="refGenomeSource.genomeSource">
+            <when value="indexed">
+              <action type="metadata" name="dbkey">
+                <option type="from_data_table" name="sam_fa_indexes" column="1" offset="0">
+                  <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
+                  <filter type="param_value" ref="refGenomeSource.index" column="0"/>
+                </option>
+              </action>
+            </when>
+            <when value="history">
+              <action type="metadata" name="dbkey">
+                <option type="from_param" name="refGenomeSource.ownFile" param_attribute="dbkey" />
+              </action>
+            </when>
+          </conditional>
+        </actions>
+      </data>
+  </outputs>
+</tool>
diff -r 5a3f8b0b80f9 -r 9266d807ca85 galaxy-conf/MapDyads.xml
--- a/galaxy-conf/MapDyads.xml	Tue Feb 28 15:39:16 2012 -0500
+++ b/galaxy-conf/MapDyads.xml	Tue Mar 06 21:55:46 2012 -0500
@@ -28,7 +28,7 @@
 <help>
 .. class:: warningmark
 
-  This tool requires sequencing reads in BAM format. If your reads are in SAM format, use the SAM-to-BAM tool under NGS: SAMTools.
+  This tool requires sequencing reads in SAM, BAM, Bed format.
 
 .. class:: warningmark
 
diff -r 5a3f8b0b80f9 -r 9266d807ca85 galaxy-conf/MovingAverageSmooth.xml
--- a/galaxy-conf/MovingAverageSmooth.xml	Tue Feb 28 15:39:16 2012 -0500
+++ b/galaxy-conf/MovingAverageSmooth.xml	Tue Mar 06 21:55:46 2012 -0500
@@ -1,4 +1,4 @@
-<tool id="GaussianSmoother" name="Gaussian smooth" version="1.0.0">
+<tool id="MovingAverageSmoother" name="Moving average smooth" version="1.0.0">
   <description>a (Big)Wig file</description>
   <command interpreter="sh">galaxyToolRunner.sh wigmath.MovingAverageSmooth -i $input -w $W -o $output</command>
   <inputs>
diff -r 5a3f8b0b80f9 -r 9266d807ca85 galaxy-conf/RollingReadLength.xml
--- a/galaxy-conf/RollingReadLength.xml	Tue Feb 28 15:39:16 2012 -0500
+++ b/galaxy-conf/RollingReadLength.xml	Tue Mar 06 21:55:46 2012 -0500
@@ -11,7 +11,7 @@
 <help>
 .. class:: warningmark
 
-This tool requires paired-end BAM formatted data. Using single-end data will result in a constant read length.
+This tool requires paired-end SAM, BAM, or Bed formatted data. Using single-end data will result in a constant read length.
 
 .. class:: warningmark
 
diff -r 5a3f8b0b80f9 -r 9266d807ca85 galaxy-conf/ZScore.xml
--- a/galaxy-conf/ZScore.xml	Tue Feb 28 15:39:16 2012 -0500
+++ b/galaxy-conf/ZScore.xml	Tue Mar 06 21:55:46 2012 -0500
@@ -39,10 +39,4 @@
 	    <output name="output" file="zscorer.output3"/>
 	  </test>-->
   </tests>
-  
-<help>
-.. class:: warningmark
-
-This tool was contributed by Timothy Palpant.
-</help>
 </tool>
diff -r 5a3f8b0b80f9 -r 9266d807ca85 lib/dnaproperties-1732.jar
Binary file lib/dnaproperties-1732.jar has changed
diff -r 5a3f8b0b80f9 -r 9266d807ca85 lib/java-genomics-io.jar
Binary file lib/java-genomics-io.jar has changed