# HG changeset patch
# User bgruening
# Date 1386695598 18000
# Node ID c53a73b8eef9d2ecce9d100a02f260d84c775467
# Parent  1c5ed9126db68db23a05629f0f6eaec4d56228e8
Uploaded

diff -r 1c5ed9126db6 -r c53a73b8eef9 bamCompare.xml
--- a/bamCompare.xml	Wed Dec 04 05:50:46 2013 -0500
+++ b/bamCompare.xml	Tue Dec 10 12:13:18 2013 -0500
@@ -70,7 +70,7 @@
         <param name="bamFile1" format="bam" type="data" label="Treatment BAM file"
             help="The BAM file must be sorted."/>
 
-        <param name="bamFile2" format="bam" type="data" label="Input BAM file"
+        <param name="bamFile2" format="bam" type="data" label="BAM file"
             help="The BAM file must be sorted."/>
 
         <param name="fragmentLength" type="integer" value="300" min="1"
diff -r 1c5ed9126db6 -r c53a73b8eef9 bamCoverage.xml
--- a/bamCoverage.xml	Wed Dec 04 05:50:46 2013 -0500
+++ b/bamCoverage.xml	Tue Dec 10 12:13:18 2013 -0500
@@ -48,7 +48,7 @@
     </command>
 
     <inputs>
-        <param name="bamInput" format="bam" type="data" label="Input BAM file"
+        <param name="bamInput" format="bam" type="data" label="BAM file"
             help="The BAM file must be sorted."/>
 
         <param name="fragmentLength" type="integer" value="300" min="1"
diff -r 1c5ed9126db6 -r c53a73b8eef9 bigwigCompare.xml
--- a/bigwigCompare.xml	Wed Dec 04 05:50:46 2013 -0500
+++ b/bigwigCompare.xml	Tue Dec 10 12:13:18 2013 -0500
@@ -35,7 +35,7 @@
     </stdio>
     <inputs>
         <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
-        <param name="bigwigFile2" format="bigwig" type="data" label="Input bigwig file" />
+        <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" />
 
         <param name="comparison_type" type="select" 
                 label="How to compare the two files"
diff -r 1c5ed9126db6 -r c53a73b8eef9 computeGCBias.xml
--- a/computeGCBias.xml	Wed Dec 04 05:50:46 2013 -0500
+++ b/computeGCBias.xml	Tue Dec 10 12:13:18 2013 -0500
@@ -58,7 +58,7 @@
     </command>
     <inputs>
 
-        <param name="bamInput" format="bam" type="data" label="Input BAM file"
+        <param name="bamInput" format="bam" type="data" label="BAM file"
             help="The BAM file must be sorted."/>
 
         <expand macro="reference_genome_source" />
diff -r 1c5ed9126db6 -r c53a73b8eef9 computeMatrix.xml
--- a/computeMatrix.xml	Wed Dec 04 05:50:46 2013 -0500
+++ b/computeMatrix.xml	Tue Dec 10 12:13:18 2013 -0500
@@ -115,10 +115,11 @@
       
       <when value="reference-point">
         <param name="referencePoint" type="select" label="The reference point for the plotting">
-        <option value="TSS" selected="true">region start (TSS)</option>
-        <option value="TES" selected="true">region end (TES)</option>
-        <option value="center" selected="true">center of the region</option>
+            <option value="TSS" selected="true">beginning of region (e.g. TSS)</option>
+            <option value="TES">end of region (e.g. TES)</option>
+            <option value="center">center of region</option>
         </param>
+        
         <param name="nanAfterEnd" type="boolean" truevalue="--nanAfterEnd" falsevalue="" label="Discard any values after the region end" help="This is useful to visualize the region end when not using the scale-regions mode and when the reference-point is set to the TSS."/>
         <param name="beforeRegionStartLength" type="integer" value="1000" min="1" label="Distance upstream of the start site of the regions defined in the region file" help="If the regions are genes, this would be the distance upstream of the transcription start site."/>
         
@@ -128,15 +129,15 @@
     
     <conditional name="output" >
         <param name="showOutputSettings" type="select" label="Show additional output options" >
-        <option value="no" selected="true">no</option>
-        <option value="yes">yes</option>
-      </param>
-      <when value="no" />
-      <when value="yes">
-        <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/>
-        <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/>
-        <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
-    </when>
+            <option value="no" selected="true">no</option>
+            <option value="yes">yes</option>
+        </param>
+          <when value="no" />
+          <when value="yes">
+            <param name="saveData" type="boolean" label="Save the averages per matrix column into a text file" help="This corresponds to the underlying data used to plot a summary profile."/>
+            <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap" help="This matrix can easily be loaded into R or other programs."/>
+            <param name="saveSortedRegions" type="boolean" label="Save the regions after skiping zeros or min/max threshold values" help="The order of the regions in the file follows the sorting order selected. This is useful, for example, to generate other heatmaps keeping the sorting of the first heatmap."/>
+        </when>
     </conditional>
 
     <conditional name="advancedOpt" >
@@ -182,17 +183,32 @@
     
     </inputs>
   <outputs>
-    <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: matrix">
+    <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix">
     </data>
-    <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: raw data">
-      <filter>(output['showOutputSettings'] == 'yes' and output['saveData'] == True)</filter>
+    <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
+        <filter>
+        ((
+            output['showOutputSettings'] == 'yes' and 
+            output['saveData'] is True
+        ))
+        </filter>
     </data>
-    <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: matrix of values">
-      <filter>(output['showOutputSettings'] == 'yes' and output['saveMatrix'] == True)</filter>
+    <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
+        <filter>
+        ((
+            output['showOutputSettings'] == 'yes' and 
+            output['saveMatrix'] is True
+        ))
+        </filter>
     </data>
     <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
-      <filter>(output['showOutputSettings'] == 'yes' and output['saveSortedRegions'] == True)</filter>
-    </data>  
+        <filter>
+        ((
+            output['showOutputSettings'] == 'yes' and 
+            output['saveSortedRegions'] is True
+        ))
+        </filter>
+    </data>
   </outputs>
     <!--
     computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 
diff -r 1c5ed9126db6 -r c53a73b8eef9 correctGCBias.xml
--- a/correctGCBias.xml	Wed Dec 04 05:50:46 2013 -0500
+++ b/correctGCBias.xml	Tue Dec 10 12:13:18 2013 -0500
@@ -50,7 +50,7 @@
 
   <param name="GCbiasFrequenciesFile" type="data" format="tabular" label="Output of computeGCBias" />
 
-  <param name="bamInput" format="bam" type="data" label="Input BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
+  <param name="bamInput" format="bam" type="data" label="BAM file" help="This should be same file that was used for computeGCbias. The BAM file must be sorted."/>
 
         <expand macro="reference_genome_source" />
         <expand macro="effectiveGenomeSize" />
diff -r 1c5ed9126db6 -r c53a73b8eef9 deepTools_macros.xml
--- a/deepTools_macros.xml	Wed Dec 04 05:50:46 2013 -0500
+++ b/deepTools_macros.xml	Tue Dec 10 12:13:18 2013 -0500
@@ -43,11 +43,13 @@
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
             <requirement type="package" >ucsc_tools</requirement>
-            <requirement type="package" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">deepTools</requirement>
+            <requirement type="package" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">deepTools</requirement>
             <requirement type="package" version="0.1">ucsc_tools</requirement>
             <requirement type="package" version="1.7.1">numpy</requirement>
             <requirement type="package" version="0.7.7">pysam</requirement>
+            <requirement type="package" version="1.2.1">matplotlib</requirement>
             <requirement type="package" version="0.1.19">samtools</requirement>
+            <requirement type="package" version="12-2013">bx-python</requirement>
             <yield />
         </requirements>
         </macro>
@@ -68,7 +70,7 @@
     </token>
 
     <macro name="multiple_input_bams">
-        <repeat name="input_files" title="Input files" min="2">
+        <repeat name="input_files" title="BAM files" min="2">
             <param name="bamfile" type="data" format="bam" 
                 label="Bam file" 
                 help="The BAM file must be sorted."/>
diff -r 1c5ed9126db6 -r c53a73b8eef9 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Dec 04 05:50:46 2013 -0500
+++ b/tool_dependencies.xml	Tue Dec 10 12:13:18 2013 -0500
@@ -1,19 +1,22 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="samtools" version="0.1.19">
-        <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="00e17a794a2e" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.7.1">
-        <repository changeset_revision="796c0081adad" name="package_numpy_1_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="796c0081adad" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="matplotlib" version="1.2.1">
-        <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="9d164359606b" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.12.0">
-        <repository changeset_revision="d277bf006c3e" name="package_scipy_0_12" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="d277bf006c3e" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="pysam" version="0.7.7">
-        <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bx-python" version="12-2013">
+        <repository changeset_revision="f938170835cc" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="ucsc_tools" version="0.1">
@@ -54,7 +57,7 @@
          <readme>The tools downloaded by this dependency definition are free for academic use. TODO: UCSC tools are only available with their latest version. That is not good for reproducibility.</readme>
      </package>
 
-    <package name="deepTools" version="1.5.1_323fa6bf083c9d40e5092a6364a4ab8fee57507a">
+    <package name="deepTools" version="1.5.4_fada41ab04f78c4c78d10c7a216e5c3160e8c36e">
         <install version="1.0">
             <actions>
                 <action type="shell_command">git clone --recursive https://github.com/fidelram/deepTools.git</action>
@@ -63,8 +66,11 @@
                     <repository changeset_revision="b62538c8c664" name="package_pysam_0_7_7" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
                         <package name="pysam" version="0.7.7" />
                     </repository>
+                    <repository changeset_revision="f938170835cc" name="package_bx_python_12_2013" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu">
+                        <package name="bx-python" version="12-2013" />
+                    </repository>
                 </action>
-                <action type="shell_command">git reset --hard 323fa6bf083c9d40e5092a6364a4ab8fee57507a</action>
+                <action type="shell_command">git reset --hard fada41ab04f78c4c78d10c7a216e5c3160e8c36e</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>
                 <action type="shell_command">
                     export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
@@ -78,6 +84,9 @@
                 </action>
              </actions>
          </install>
-         <readme>Installation of deepTools from Fidel Ramirez.</readme>
+         <readme>
+            Installation of deepTools from Fidel Ramirez.
+            https://github.com/fidelram/deepTools
+         </readme>
      </package>
 </tool_dependency>