# HG changeset patch
# User bgruening
# Date 1387055591 18000
# Node ID f996339050ac85733322535cdb641efe280d6248
# Parent  b51c11c78640c70a06a1c5d010e7e579e677dccc
Uploaded

diff -r b51c11c78640 -r f996339050ac computeMatrix.xml
--- a/computeMatrix.xml	Sat Dec 14 14:14:22 2013 -0500
+++ b/computeMatrix.xml	Sat Dec 14 16:13:11 2013 -0500
@@ -120,15 +120,15 @@
             <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."/>
-        
         <param name="afterRegionStartLength" type="integer" value="1000" min="1" label="Distance downstream of the end site of the given regions" help="If the regions are genes, this would be the distance downstream of the transcription end site."/>
       </when>
     </conditional>
 
-    <expand macro="graphic_output_settings" />
+    <expand macro="input_graphic_output_settings">
+        <expand macro="input_save_matrix_values" />
+    </expand>
 
     <conditional name="advancedOpt" >
       <param name="showAdvancedOpt" type="select" label="Show advanced options" >
@@ -175,6 +175,7 @@
   <outputs>
     <data format="bgzip" name="outFileName" label="${tool.name} on ${on_string}: Matrix" />
     <expand macro="output_graphic_outputs" />
+    <expand macro="output_save_matrix_values" />
   </outputs>
     <!--
     computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 
diff -r b51c11c78640 -r f996339050ac deepTools_macros.xml
--- a/deepTools_macros.xml	Sat Dec 14 14:14:22 2013 -0500
+++ b/deepTools_macros.xml	Sat Dec 14 16:13:11 2013 -0500
@@ -1,5 +1,5 @@
 <macros>
-    <macro name="bamCorrelate_mode_actions">
+    <xml name="bamCorrelate_mode_actions">
         <conditional name="advancedOpt">
             <param name="showAdvancedOpt" type="select" label="Show advanced options" >
                 <option value="no" selected="true">no</option>
@@ -36,9 +36,9 @@
                 <expand macro="colormap" />
             </when>
         </conditional>
-    </macro>
+    </xml>
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <macro name="requirements">
+    <xml name="requirements">
         <requirements>
             <requirement type="package" >samtools</requirement>
             <requirement type="package" >deepTools</requirement>
@@ -50,21 +50,20 @@
             <requirement type="package" version="0.12.0">scipy</requirement>
             <requirement type="package" version="1.2.1">matplotlib</requirement>
             <requirement type="package" version="0.1.19">samtools</requirement>
-            <requirement type="package" version="0.7.1">bx-python</requirement>
+            <requirement type="package" version="12-2013">bx-python</requirement>
             <yield />
         </requirements>
-    </macro>
-    <macro name="stdio">
+    </xml>
+    <xml name="stdio">
         <stdio>
             <exit_code range="1:" />
             <exit_code range=":-1" />
-            <exit_code range="0" level="warning" description="Warning" />
             <regex match="Error:" />
             <regex match="Exception:" />
             <regex match="EXception:" />
             <regex match="Traceback" />
         </stdio>
-    </macro>
+    </xml>
     <token name="@REFERENCES@">
 
 For more informations, please visit our `project site`_.
@@ -80,7 +79,7 @@
 
     </token>
 
-    <macro name="multiple_input_bams">
+    <xml name="multiple_input_bams">
         <repeat name="input_files" title="BAM files" min="2">
             <param name="bamfile" type="data" format="bam" 
                 label="Bam file" 
@@ -89,7 +88,7 @@
                 label="Label"
                 help="Label to use in the output. If not given the dataset name will be used instead."/>
           </repeat>
-    </macro>
+    </xml>
 
     <token name="@multiple_input_bams@">
         #for $i in $input_files:
@@ -109,7 +108,7 @@
         #end for
     </token>
 
-    <macro name="reference_genome_source">
+    <xml name="reference_genome_source">
         <conditional name="source">
             <param name="ref_source" type="select" label="Reference genome">
                 <option value="cached">locally cached</option>
@@ -127,7 +126,7 @@
                 <param name="input1" type="data" format="twobit" label="Select a reference dataset in 2bit format" />
             </when>
         </conditional>
-    </macro>
+    </xml>
 
     <token name="@reference_genome_source@">
     #if $source.ref_source=="history":
@@ -137,7 +136,7 @@
     #end if
     </token>
 
-    <macro name="effectiveGenomeSize">
+    <xml name="effectiveGenomeSize">
         <conditional name="effectiveGenomeSize">
             <param name="effectiveGenomeSize_opt" type="select" label="Effective genome size"
                 help="The effective genome size is the portion of the genome that is mappable. Large fractions of the genome are stretches of NNNN that should be discarded. 
@@ -153,9 +152,9 @@
                 <param name="effectiveGenomeSize" type="integer" value="" label="Effective genome size" />
             </when>
         </conditional>
-    </macro>
+    </xml>
 
-    <macro name="image_file_format">
+    <xml name="image_file_format">
         <param name="outFileFormat" type="select" label="Image file format">
             <option value="png" selected="true">png</option>
             <option value="pdf">pdf</option>
@@ -163,9 +162,13 @@
             <option value="eps">eps</option>
             <option value="emf">emf</option>
         </param>
-    </macro>
+    </xml>
 
-    <macro name="graphic_output_settings">
+    <xml name="input_save_matrix_values">
+        <param name="saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
+    </xml>
+
+    <xml name="input_graphic_output_settings">
         <conditional name="output" >
             <param name="showOutputSettings" type="select" label="Show advanced output settings" >
                 <option value="no" selected="true">no</option>
@@ -174,14 +177,13 @@
             <when value="no" />
             <when value="yes">
                 <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="saveData" type="boolean" label="Save the data underlying the average profile"/>
                 <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."/>
             </when>
         </conditional>
-    </macro>
+    </xml>
 
-    <macro name="input_image_file_format">
+    <xml 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>
@@ -189,9 +191,9 @@
             <option value="eps">eps</option>
             <option value="emf">emf</option>
         </param>
-    </macro>
+    </xml>
 
-    <macro name="output_image_file_format">
+    <xml name="output_image_file_format">
         <data format="png" name="outFileName" label="${tool.name} image">
             <change_format>
                 <when input="output.outFileFormat" value="pdf" format="pdf" />
@@ -200,10 +202,20 @@
                 <when input="output.outFileFormat" value="emf" format="emf" />
             </change_format>
         </data>
-    </macro>
+    </xml>
 
-    <macro name="output_graphic_outputs">
-        <yield />
+    <xml name="output_save_matrix_values">
+        <data format="tabular" name="outFileNameMatrix" label="${tool.name} on ${on_string}: Heatmap values">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and 
+                output['saveMatrix'] is True
+            ))
+            </filter>
+        </data>
+    </xml>
+
+    <xml name="output_graphic_outputs">
         <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
             <filter>
             ((
@@ -212,14 +224,6 @@
             ))
             </filter>
         </data>
-        <data format="tabular" name="outFileNameMatrix" label="${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>
             ((
@@ -228,9 +232,9 @@
             ))
             </filter>
         </data>
-    </macro>
+    </xml>
 
-    <macro name="colormap">
+    <xml name="colormap">
         <param name="colorMap" type="select" label="Color map to use for the heatmap" help=" Available color map names can be found here: http://www.astro.lsa.umich.edu/~msshin/science/code/matplotlib_cm/">
             <option value="RdYlBu" selected="true">RdYlBu</option>
             <option value="Accent">Accent</option>
@@ -372,6 +376,6 @@
             <option value="afmhot_r">afmhot reversed</option>
         </param>
 
-    </macro>
+    </xml>
 
 </macros>
diff -r b51c11c78640 -r f996339050ac heatmapper.xml
--- a/heatmapper.xml	Sat Dec 14 14:14:22 2013 -0500
+++ b/heatmapper.xml	Sat Dec 14 16:13:11 2013 -0500
@@ -91,8 +91,9 @@
     <inputs>
         <param name="matrixFile" format="bgzip" type="data" label="Matrix file from the computeMatrix tool"/>
 
-        <expand macro="graphic_output_settings">
+        <expand macro="input_graphic_output_settings">
             <expand macro="input_image_file_format" />
+            <expand macro="input_save_matrix_values" />
         </expand>
 
         <conditional name="advancedOpt" >
@@ -176,9 +177,9 @@
         </conditional>
     </inputs>
     <outputs>
-        <expand macro="output_graphic_outputs">
-            <expand macro="output_image_file_format" />
-        </expand>
+        <expand macro="output_image_file_format" />
+        <expand macro="output_graphic_outputs" />
+        <expand macro="output_save_matrix_values" />
     </outputs>
     <tests>
         <test>
diff -r b51c11c78640 -r f996339050ac profiler.xml
--- a/profiler.xml	Sat Dec 14 14:14:22 2013 -0500
+++ b/profiler.xml	Sat Dec 14 16:13:11 2013 -0500
@@ -20,10 +20,6 @@
                 --outFileNameData '$outFileNameData' 
             #end if
 
-            #if $output.saveMatrix:
-                --outFileNameMatrix '$outFileNameMatrix'
-            #end if
-
             #if $output.saveSortedRegions:
                 --outFileSortedRegions '$outFileSortedRegions'
             #end if
@@ -79,7 +75,7 @@
             </when>
         </conditional>
 
-        <expand macro="graphic_output_settings">
+        <expand macro="input_graphic_output_settings">
             <expand macro="input_image_file_format" />
         </expand>
 
@@ -122,9 +118,8 @@
         </conditional>
     </inputs>
     <outputs>
-        <expand macro="output_graphic_outputs">
-            <expand macro="output_image_file_format" />
-        </expand>
+        <expand macro="output_image_file_format" />
+        <expand macro="output_graphic_outputs" />
     </outputs>
     <help>
 
diff -r b51c11c78640 -r f996339050ac tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Dec 14 14:14:22 2013 -0500
+++ b/tool_dependencies.xml	Sat Dec 14 16:13:11 2013 -0500
@@ -15,8 +15,8 @@
     <package name="pysam" version="0.7.7">
         <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="bx-python" version="0.7.1">
-        <repository changeset_revision="f2ce8530a6b6" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    <package name="bx-python" version="12-2013">
+        <repository changeset_revision="5457e32b427c" name="package_bx_python_12_2013" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
     </package>
 
     <package name="ucsc_tools" version="0.1">
@@ -66,8 +66,8 @@
                     <repository changeset_revision="240d1ad9f207" name="package_pysam_0_7_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="pysam" version="0.7.7" />
                     </repository>
-                    <repository changeset_revision="f2ce8530a6b6" name="package_bx_python_0_7" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="bx-python" version="0.7.1" />
+                    <repository changeset_revision="5457e32b427c" 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" />