# HG changeset patch
# User bgruening
# Date 1387038118 18000
# Node ID df9f0dbb1d2aca29dad7e815655bdeff67e4389b
# Parent  e43b4015b4ccb6e633aa12c4e7e28212813818b3
Uploaded

diff -r e43b4015b4cc -r df9f0dbb1d2a bamCorrelate.xml
--- a/bamCorrelate.xml	Fri Dec 13 17:38:30 2013 -0500
+++ b/bamCorrelate.xml	Sat Dec 14 11:21:58 2013 -0500
@@ -107,13 +107,7 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="outFileFormat" type="select" label="Image file format">
-                    <option value="png" selected="true">png</option>
-                    <option value="pdf">pdf</option>
-                    <option value="svg">svg</option>
-                    <option value="eps">eps</option>
-                    <option value="emf">emf</option>
-                </param>
+                <expand macro="input_image_file_format"/>
                 <param name="saveRawCounts" type="boolean" label="Save the bin counts"/>
                 <param name="saveCorMatrix" type="boolean" label="Save the correlation matrix"/>
             </when>
@@ -121,14 +115,7 @@
 
     </inputs>
     <outputs>
-        <data format="png" name="outFileName">
-            <change_format>
-                <when input="output.outFileFormat" value="pdf" format="pdf" />
-                <when input="output.outFileFormat" value="svg" format="svg" />
-                <when input="output.outFileFormat" value="eps" format="eps" />
-                <when input="output.outFileFormat" value="emf" format="emf" />
-            </change_format>
-        </data>
+        <expand macro="output_image_file_format" />
         <data format="tabular" name="outFileRawCounts" label="${tool.name} on ${on_string}: bin counts">
             <filter>(outputOpt['showOutputOpt'] == 'yes' and outputOpt['saveRawCounts'] == True)</filter>
         </data>
diff -r e43b4015b4cc -r df9f0dbb1d2a deepTools_macros.xml
--- a/deepTools_macros.xml	Fri Dec 13 17:38:30 2013 -0500
+++ b/deepTools_macros.xml	Sat Dec 14 11:21:58 2013 -0500
@@ -62,6 +62,7 @@
             <regex match="Error:" />
             <regex match="Exception:" />
             <regex match="EXception:" />
+            <regex match="Traceback" />
         </stdio>
     </macro>
     <token name="@REFERENCES@">
@@ -172,13 +173,7 @@
             </param>
             <when value="no" />
             <when value="yes">
-                <param name="outFileFormat" type="select" label="Image file format">
-                    <option value="png" selected="true">png</option>
-                    <option value="pdf">pdf</option>
-                    <option value="svg">svg</option>
-                    <option value="eps">eps</option>
-                    <option value="emf">emf</option>
-                </param>
+                <yield />
                 <param name="saveData" type="boolean" label="Save the data underlying data for the average profile"/>
                 <param name="saveMatrix" type="boolean" label="Save the the matrix of values underlying the heatmap"/>
                 <param name="saveSortedRegions" type="boolean" label="Save the regions after skipping 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."/>
@@ -186,7 +181,17 @@
         </conditional>
     </macro>
 
-    <macro name="output_graphic_outputs">
+    <macro name="input_image_file_format">
+        <param name="outFileFormat" type="select" label="Image file format">
+            <option value="png" selected="true">png</option>
+            <option value="pdf">pdf</option>
+            <option value="svg">svg</option>
+            <option value="eps">eps</option>
+            <option value="emf">emf</option>
+        </param>
+    </macro>
+
+    <macro name="output_image_file_format">
         <data format="png" name="outFileName" label="${tool.name} image">
             <change_format>
                 <when input="output.outFileFormat" value="pdf" format="pdf" />
@@ -195,6 +200,10 @@
                 <when input="output.outFileFormat" value="emf" format="emf" />
             </change_format>
         </data>
+    </macro>
+
+    <macro name="output_graphic_outputs">
+        <yield />
         <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
             <filter>
             ((
diff -r e43b4015b4cc -r df9f0dbb1d2a heatmapper.xml
--- a/heatmapper.xml	Fri Dec 13 17:38:30 2013 -0500
+++ b/heatmapper.xml	Sat Dec 14 11:21:58 2013 -0500
@@ -79,12 +79,21 @@
             #end if
 
             $advancedOpt.onePlotPerGroup
+
+            #if $advancedOpt.clustering.clustering_options == 'kmeans':
+                #if int($advancedOpt.clustering.k_kmeans) > 0:
+                    --kmeans $advancedOpt.clustering.k_kmeans
+                #end if
+            #end if
+
         #end if
     </command>
     <inputs>
         <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
 
-        <expand macro="graphic_output_settings" />
+        <expand macro="graphic_output_settings">
+            <expand macro="input_image_file_format" />
+        </expand>
 
         <conditional name="advancedOpt" >
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -149,19 +158,27 @@
                 <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, &quot;label1, label2&quot;."/>
                 <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." />
                 <param name="onePlotPerGroup" type="boolean" truevalue="--onePlotPerGroup" falsevalue="" label="Do one plot per group" help="When the region file contains groups separated by &quot;#&quot;, the default is to plot the averages for the distinct plots in one plot. If this option is set, each group will get its own plot, stacked on top of each other."/>
+
+                <conditional name="clustering">
+                    <param name="clustering_options" type="select" label="Clustering algorithm">
+                        <option value="none">No clustering</option>
+                        <option value="kmeans">Kmeans clustering</option>
+                    </param>
+                    <when value="kmeans">
+                        <param name="k_kmeans" type="integer" value="0" label="Number of clusters to compute" 
+                            help="When this option is set, then the matrix is split into clusters using the kmeans algorithm. Only works for data that is not grouped, otherwise only the first group will be clustered. If more specific clustering methods are required it is advisable to save the underlying matrix and run the clustering using other software. The plotting of the clustering may fail (Error: Segmentation fault) if a cluster has very few members compared to the total number or regions. (default: None)."/>
+                    </when>
+                    <when value="none" />
+                </conditional>
+
+
             </when>
         </conditional>
     </inputs>
     <outputs>
-        <data format="png" name="outFileName" label="${tool.name} image">
-            <change_format>
-                <when input="output.outFileFormat" value="pdf" format="pdf" />
-                <when input="output.outFileFormat" value="svg" format="svg" />
-                <when input="output.outFileFormat" value="eps" format="eps" />
-                <when input="output.outFileFormat" value="emf" format="emf" />
-            </change_format>
-        </data>
-        <expand macro="output_graphic_outputs" />
+        <expand macro="output_graphic_outputs">
+            <expand macro="output_image_file_format" />
+        </expand>
     </outputs>
     <tests>
         <test>
diff -r e43b4015b4cc -r df9f0dbb1d2a profiler.xml
--- a/profiler.xml	Fri Dec 13 17:38:30 2013 -0500
+++ b/profiler.xml	Sat Dec 14 11:21:58 2013 -0500
@@ -80,8 +80,8 @@
         </conditional>
 
         <expand macro="graphic_output_settings">
-            <expand macro="image_file_format" />
-        <expand>
+            <expand macro="input_image_file_format" />
+        </expand>
 
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -122,7 +122,9 @@
         </conditional>
     </inputs>
     <outputs>
-        <expand macro="output_graphic_outputs" />
+        <expand macro="output_graphic_outputs">
+            <expand macro="output_image_file_format" />
+        </expand>
     </outputs>
     <help>
 
diff -r e43b4015b4cc -r df9f0dbb1d2a tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Dec 13 17:38:30 2013 -0500
+++ b/tool_dependencies.xml	Sat Dec 14 11:21:58 2013 -0500
@@ -69,6 +69,15 @@
                     <repository changeset_revision="efba2bb75ac8" name="package_bx_python_12_2013" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="bx-python" version="12-2013" />
                     </repository>
+                    <repository changeset_revision="84125ffacb90" name="package_numpy_1_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="numpy" version="1.7.1" />
+                    </repository>
+                    <repository changeset_revision="966f29c955b9" name="package_matplotlib_1_2" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="matplotlib" version="1.2.1" />
+                    </repository>
+                    <repository changeset_revision="3c1bf479158c" name="package_scipy_0_12" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
+                        <package name="scipy" version="0.12.0" />
+                    </repository>
                 </action>
                 <action type="shell_command">git reset --hard 6765c227d9628f8e6ba690e6fde7f1d86c497b49</action>
                 <action type="make_directory">$INSTALL_DIR/lib/python</action>