# HG changeset patch
# User bgruening
# Date 1450861226 18000
# Node ID 451e73bf38fe72a14058b7f0deaad0b5a89d9af5
# Parent  345a9a2281e0cd57cb7185325e00592c4688a71b
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 54a10cf268ca9a5399f13458a1b218be7891bd41

diff -r 345a9a2281e0 -r 451e73bf38fe computeMatrix.xml
--- a/computeMatrix.xml	Tue Dec 22 13:47:40 2015 -0500
+++ b/computeMatrix.xml	Wed Dec 23 04:00:26 2015 -0500
@@ -1,5 +1,5 @@
 <tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0">
-    <description>prepares data for plotting a heatmap or a profile of given regions</description>
+    <description>preparation step to plot a heatmap or a profile</description>
     <macros>
         <token name="@BINARY@">computeMatrix</token>
         <import>deepTools_macros.xml</import>
@@ -9,22 +9,28 @@
 <![CDATA[
         #import tempfile
 
+        #for $rf in $regionsFiles:
+            cat "$rf.regionsFile" >> ./temp_input_path;
+            #if str($rf.label.value).strip():
+                echo "\#$rf.label.value" >> ./temp_input_path;
+            #else:
+                echo "\#$rf.regionsFile.name" >> ./temp_input_path;
+            #end if
+        #end for
+
         @BINARY@
 
             $mode.mode_select
-            --regionsFileName
-            #for $rf in $regionsFiles:
-                '$rf.regionsFile' 
-            #end for
-            --scoreFileName
-            #for $bw in $scoreFileName:
-                '$bw' 
-            #end for
+            --regionsFileName ./temp_input_path
+            --scoreFileName '$scoreFile'
             --outFileName '$outFileName'
 
             @THREADS@
 
             #if $output.showOutputSettings == "yes"
+                #if $output.saveData:
+                    --outFileNameData '$outFileNameData' 
+                #end if
                 #if $output.saveMatrix:
                 --outFileNameMatrix '$outFileNameMatrix'
                 #end if
@@ -79,12 +85,12 @@
                 help="Label to use in the output."/>
         </repeat>
 
-        <param name="scoreFileName" format="bigwig" type="data"
-            label="Score file" multiple="True"
+        <param name="scoreFile" format="bigwig" type="data"
+            label="Score file"
             help="Should be a bigWig file (containing a score, usually covering
             the whole genome). You can generate a bigWig file either from a
             bedGraph or WIG file using UCSC tools or from a BAM file using the
-            deepTool bamCoverage. (--scoreFileName)"/>
+            deepTool bamCoverage. (-scoreFile)"/>
 
         <conditional name="mode" >
             <param name="mode_select" type="select"
@@ -208,12 +214,12 @@
         <expand macro="output_save_matrix_values" />
     </outputs>
     <!--
-    computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1
+    computeMatrix -S test.bw -R test2.bed -a 100 -b 100 -bs 1 
     -->
     <tests>
         <test>
             <param name="regionsFile" value="computeMatrix1.bed" ftype="bed" />
-            <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
+            <param name="scoreFile" value="bamCoverage_result4.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="reference-point" />
             <param name="binSize" value="10" />
@@ -226,7 +232,7 @@
         </test>
         <test>
             <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
-            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
+            <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="reference-point" />
             <param name="binSize" value="10" />
@@ -236,7 +242,7 @@
         </test>
         <test>
             <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
-            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
+            <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="scale-regions" />
             <param name="endLabel" value="END" />
@@ -265,7 +271,7 @@
    :alt: Relationship between computeMatrix, heatmapper and profiler
 
 
-You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/computeMatrix.html
+You can find more details on the computeMatrix wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix
 
 
 -----
diff -r 345a9a2281e0 -r 451e73bf38fe deepTools_macros.xml
--- a/deepTools_macros.xml	Tue Dec 22 13:47:40 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 04:00:26 2015 -0500
@@ -40,10 +40,10 @@
     </xml>
 
     <token name="@HEATMAP_OPTIONS@">
-        #if str($plotting_type.zMin) != "":
+        #if $plotting_type.zMin:
             --zMin $plotting_type.zMin
         #end if
-        #if str($plotting_type.zMax) != "":
+        #if $plotting_type.zMax:
             --zMax $plotting_type.zMax
         #end if
         --colorMap '$plotting_type.colorMap'
@@ -107,11 +107,7 @@
                     </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: 0 [do not cluster])."/>
+                            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>
@@ -412,6 +408,7 @@
             <when value="no" />
             <when value="yes">
                 <yield />
+                <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>
@@ -459,6 +456,14 @@
     </xml>
 
     <xml name="output_graphic_outputs">
+        <data format="tabular" name="outFileNameData" label="${tool.name} on ${on_string}: averages per matrix column">
+            <filter>
+            ((
+                output['showOutputSettings'] == 'yes' and
+                output['saveData'] is True
+            ))
+            </filter>
+        </data>
         <data format="bed" name="outFileSortedRegions" label="${tool.name} on ${on_string}: sorted/filtered regions">
             <filter>
             ((
diff -r 345a9a2281e0 -r 451e73bf38fe static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r 345a9a2281e0 -r 451e73bf38fe test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 345a9a2281e0 -r 451e73bf38fe test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 345a9a2281e0 -r 451e73bf38fe test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Tue Dec 22 13:47:40 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 04:00:26 2015 -0500
@@ -5,4 +5,4 @@
 chrM	220	230	7690304.31
 chrM	230	240	6027535.81
 chrM	240	250	3325537.00
-chrM	250	16569	623538.2
+chrM	250	260	623538.19
diff -r 345a9a2281e0 -r 451e73bf38fe test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 345a9a2281e0 -r 451e73bf38fe test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed
diff -r 345a9a2281e0 -r 451e73bf38fe tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 22 13:47:40 2015 -0500
+++ b/tool_dependencies.xml	Wed Dec 23 04:00:26 2015 -0500
@@ -4,6 +4,6 @@
         <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
     <package name="deepTools" version="2.0">
-        <repository changeset_revision="747571992679" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="bd40c0aa7d8e" name="package_python_2_7_deeptools_2_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>