# HG changeset patch
# User bgruening
# Date 1422389963 18000
# Node ID 1d932daaa1987d859c95c71a02edeaf7d283d98d
# Parent  f3140d17939eb405d91f0d6596ce1bee2723defe
Uploaded

diff -r f3140d17939e -r 1d932daaa198 plotCorrelation.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/plotCorrelation.xml	Tue Jan 27 15:19:23 2015 -0500
@@ -0,0 +1,197 @@
+<tool id="deeptools_plotCorrelation" name="plotCorrelation" version="@WRAPPER_VERSION@.0">
+    <description>creates a heatmap for a score associated to genomic regions</description>
+    <expand macro="requirements"/>
+    <expand macro="stdio" />
+    <macros>
+        <token name="@BINARY@">heatmapper</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <command>
+<![CDATA[
+        heatmapper
+
+        --matrixFile $matrixFile
+        --outFileName $outFileName
+
+        #if $output.showOutputSettings == "yes"
+            --plotFileFormat $output.outFileFormat
+            #if $outFileNameData:
+                --outFileNameData '$outFileNameData'
+            #end if
+
+            #if $outFileNameMatrix:
+                --outFileNameMatrix '$outFileNameMatrix'
+            #end if
+
+            #if $outFileSortedRegions:
+                --outFileSortedRegions '$outFileSortedRegions'
+            #end if
+        #else
+            --plotFileFormat 'png'
+        #end if
+
+        #if $advancedOpt.showAdvancedOpt == "yes"
+            #if $advancedOpt.sortRegions:
+                --sortRegions '$advancedOpt.sortRegions'
+            #end if
+      
+            #if $advancedOpt.sortUsing:
+                --sortUsing '$advancedOpt.sortUsing'
+            #end if
+
+            #if $advancedOpt.averageTypeSummaryPlot:
+                --averageTypeSummaryPlot '$advancedOpt.averageTypeSummaryPlot'
+            #end if
+
+            #if str($advancedOpt.missingDataColor.value) != "None":
+                --missingDataColor '$advancedOpt.missingDataColor'
+            #end if
+
+            --colorMap '$advancedOpt.colorMap'
+
+            #if str($advancedOpt.zMin).strip() != "":
+                --zMin $advancedOpt.zMin
+            #end if
+            #if $advancedOpt.zMax:
+                --zMax $advancedOpt.zMax
+            #end if
+
+            #if str($advancedOpt.yMin).strip() != "":
+                --yMin $advancedOpt.yMin
+            #end if
+            #if $advancedOpt.yMax:
+                --yMax $advancedOpt.yMax
+            #end if
+
+            --xAxisLabel '$advancedOpt.xAxisLabel'
+            --yAxisLabel '$advancedOpt.yAxisLabel'
+
+            --heatmapWidth $advancedOpt.heatmapWidth
+            --heatmapHeight $advancedOpt.heatmapHeight
+
+            --whatToShow '$advancedOpt.whatToShow'
+
+            --startLabel '$advancedOpt.startLabel' 
+            --endLabel '$advancedOpt.endLabel'
+            --refPointLabel '$advancedOpt.referencePointLabel'
+            --regionsLabel '$advancedOpt.regionsLabel'
+
+            #if str($advancedOpt.plotTitle.value) != "None":
+                --plotTitle '$advancedOpt.plotTitle'
+            #end if
+
+            $advancedOpt.onePlotPerGroup
+
+            @KMEANS_CLUSTERING@
+
+        #end if
+]]>
+    </command>
+    <inputs>
+        <param name="corData" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
+
+        <expand macro="input_graphic_output_settings">
+            <expand macro="input_image_file_format" />
+            <expand macro="input_save_matrix_values" />
+        </expand>
+
+        <conditional name="advancedOpt" >
+            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+
+                <expand macro="colormap" />
+
+                <param name="zMin" type="float" value="" size="3"
+                    label="Minimum value for the heatmap intensities. Leave empty for automatic values"/>
+                <param name="zMax" type="float" value="" size="3"
+                    label="Maximum value for the heatmap intensities. Leave empty for automatic values"/>
+
+                <param name="plotNumbers" type="boolean" truevalue="--plotNumbers" falsevalue="" 
+                    label="Plot the correlation value" 
+                    help="If set, then the correlation number is plotted on top of the heatmap. (--plotNumbers)"/>
+
+
+
+
+                <param name="yMin" type="float" value="" size="3"
+                    label="Minimum value for the Y-axis of the summary plot. Leave empty for automatic values"/>
+                <param name="yMax" type="float" value="" size="3"
+                    label="Maximum value for Y-axis of the summary plot. Leave empty for automatic values"/>
+                <param name="xAxisLabel" type="text" value="distance from TSS (bp)" size="200"
+                    label="Description for the x-axis label" />
+                <param name="yAxisLabel" type="text" value="genes" size="30"
+                    label="Description for the y-axis label for the top panel" />
+
+                <param name="heatmapWidth" type="float" value="7.5" min="1" max="100"
+                    label="Heatmap width in cm" help="The minimum value is 1 and the maximum is 100."/>
+                <param name="heatmapHeight" type="float" value="25" min="3" max="100"
+                    label="Heatmap height in cm" help="The minimum value is 3 and the maximum is 100."/>
+
+                <param name="whatToShow" type="select" label="What to show"
+                    help ="The default is to include a summary or profile plot on top of the heatmap and a heatmap colorbar.">
+                    <option value="plot, heatmap and colorbar" selected="true">summary plot, heatmap and colorbar</option>
+                    <option value="plot and heatmap">summary plot and heatmap (no colorbar)</option>
+                    <option value="heatmap only">heatmap only</option>
+                    <option value="heatmap and colorbar">heatmap and colorbar</option>
+                    <option value="colorbar only">colorbar only</option>
+                </param>
+
+                <param name="startLabel" type="text" value="TSS" size="10"
+                    label="Label for the region start"
+                    help ="[only for scale-regions mode] Label shown in the plot for the start of the region. Default is TSS (transcription start site), but could be changed to anything, e.g. &quot;peak start&quot;." />
+                <param name="endLabel" type="text" value="TES" size="10"
+                    label="Label for the region end"
+                    help="[only for scale-regions mode] Label shown in the plot for the region end. Default is TES (transcription end site)."/>
+
+                <param name="referencePointLabel" type="text" value="TSS" size="10"
+                    label="Reference point label"
+                    help ="[only for scale-regions mode] Label shown in the plot for the reference-point. Default is the same as the reference point selected (e.g. TSS), but could be anything, e.g. &quot;peak start&quot; etc." />
+                <param name="regionsLabel" type="text" value="genes" size="30" 
+                    label="Labels for the regions plotted in the heatmap" 
+                    help="If more than one region is being plotted a list of labels separated by comma and limited by quotes, is required. For example, label1, label2.">
+                    <sanitizer>
+                        <valid initial="string.printable">
+                        </valid>
+                    </sanitizer>
+                </param>
+                <param name="plotTitle" type="text" value="" size="30"
+                    label="Title of the plot" help="Title of the plot, to be printed on top of the generated image. Leave blank for no title. (--plotTitle)" />
+                <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" 
+                    label="Do one plot per group" 
+                    help="When computeMatrix was used on more than one group of genes, the average plots for all the groups will be drawn in one panel by default. If this option is set, each group will get its own plot, stacked on top of each other."/>
+
+                <expand macro="kmeans_clustering" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <expand macro="output_image_file_format" />
+        <expand macro="output_graphic_outputs" />
+        <expand macro="output_save_matrix_values" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrixFile" value="computeMatrix_result1.gz" ftype="bgzip" />
+            <output name="outFileName" file="heatmapper_result1.png" ftype="png" compare="sim_size" delta="100" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**What it does**
+
+Tool for visualizing a correlation using either bamCorrelate or
+bigwigCorrelate. Pearson or Spearman methods are available to compute correlation
+coefficients. Results can be saved into a heat map image or as multiple
+scatter plots. Further output files are optional.
+
+-----
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>
diff -r f3140d17939e -r 1d932daaa198 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Jan 23 16:53:31 2015 -0500
+++ b/tool_dependencies.xml	Tue Jan 27 15:19:23 2015 -0500
@@ -4,22 +4,22 @@
         <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="numpy" version="1.9">
-        <repository changeset_revision="5bd85e0058d6" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="dd91d64330d4" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="matplotlib" version="1.4">
-        <repository changeset_revision="6424ce261dab" name="package_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="38e91928f905" name="package_matplotlib_1_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="scipy" version="0.14">
-        <repository changeset_revision="38e76888714c" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="a257ce4d82ad" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="pysam" version="0.8.1">
         <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="bx-python" version="0.7.2">
-        <repository changeset_revision="3134f55294b5" name="package_bx_python_0_7_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="8c4879fee3cc" name="package_bx_python_0_7_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="python" version="2.7">
-        <repository changeset_revision="dffe84445ebd" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="ucsc_tools" version="0.1">
         <install version="1.0">
@@ -66,21 +66,21 @@
                     <repository changeset_revision="6b6843e15541" name="package_pysam_0_8_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="pysam" version="0.8.1" />
                     </repository>
-                    <repository changeset_revision="3134f55294b5" name="package_bx_python_0_7_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="8c4879fee3cc" name="package_bx_python_0_7_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="bx-python" version="0.7.2" />
                     </repository>
-                    <repository changeset_revision="5bd85e0058d6" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="dd91d64330d4" name="package_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="numpy" version="1.9" />
                     </repository>
-                    <repository changeset_revision="6424ce261dab" name="package_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="38e91928f905" name="package_matplotlib_1_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="matplotlib" version="1.4" />
                     </repository>
-                    <repository changeset_revision="38e76888714c" name="package_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                    <repository changeset_revision="a257ce4d82ad" name="package_scipy_0_14" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                         <package name="scipy" version="0.14" />
                     </repository>
                 </action>
                 <action type="setup_python_environment">
-                   <repository changeset_revision="dffe84445ebd" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                   <repository changeset_revision="2c52c900e56a" name="package_python_2_7" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="python" version="2.7" />
                    </repository>
                     <!-- allow downloading and installing an Python package from https://pypi.org/ -->
@@ -89,7 +89,7 @@
 
                 <action type="set_environment">
                     <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
+                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR</environment_variable>
                     <!-- disable the config file of deepTools -->
                     <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
                 </action>