# HG changeset patch
# User bgruening
# Date 1450810060 18000
# Node ID 345a9a2281e0cd57cb7185325e00592c4688a71b
# Parent  28b07293f1ab595c85a537af7b33f4ad5f6a6837
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 8b9cdb8dc4a8fedd2b2286e7afab6529e49a9d22-dirty

diff -r 28b07293f1ab -r 345a9a2281e0 computeMatrix.xml
--- a/computeMatrix.xml	Mon Dec 21 19:10:24 2015 -0500
+++ b/computeMatrix.xml	Tue Dec 22 13:47:40 2015 -0500
@@ -1,5 +1,5 @@
 <tool id="deeptools_compute_matrix" name="computeMatrix" version="@WRAPPER_VERSION@.0">
-    <description>preparation step to plot a heatmap or a profile</description>
+    <description>prepares data for plotting a heatmap or a profile of given regions</description>
     <macros>
         <token name="@BINARY@">computeMatrix</token>
         <import>deepTools_macros.xml</import>
@@ -9,28 +9,22 @@
 <![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@
 
             $mode.mode_select
-            --regionsFileName ./temp_input_path
-            --scoreFileName '$scoreFile'
+            --regionsFileName
+            #for $rf in $regionsFiles:
+                '$rf.regionsFile' 
+            #end for
+            --scoreFileName
+            #for $bw in $scoreFileName:
+                '$bw' 
+            #end for
             --outFileName '$outFileName'
 
             @THREADS@
 
             #if $output.showOutputSettings == "yes"
-                #if $output.saveData:
-                    --outFileNameData '$outFileNameData' 
-                #end if
                 #if $output.saveMatrix:
                 --outFileNameMatrix '$outFileNameMatrix'
                 #end if
@@ -85,12 +79,12 @@
                 help="Label to use in the output."/>
         </repeat>
 
-        <param name="scoreFile" format="bigwig" type="data"
-            label="Score file"
+        <param name="scoreFileName" format="bigwig" type="data"
+            label="Score file" multiple="True"
             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. (-scoreFile)"/>
+            deepTool bamCoverage. (--scoreFileName)"/>
 
         <conditional name="mode" >
             <param name="mode_select" type="select"
@@ -214,12 +208,12 @@
         <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="scoreFile" value="bamCoverage_result4.bw" ftype="bigwig" />
+            <param name="scoreFileName" value="bamCoverage_result4.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="reference-point" />
             <param name="binSize" value="10" />
@@ -232,7 +226,7 @@
         </test>
         <test>
             <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
-            <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" />
+            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="reference-point" />
             <param name="binSize" value="10" />
@@ -242,7 +236,7 @@
         </test>
         <test>
             <param name="regionsFile" value="computeMatrix2.bed" ftype="bed" />
-            <param name="scoreFile" value="computeMatrix2.bw" ftype="bigwig" />
+            <param name="scoreFileName" value="computeMatrix2.bw" ftype="bigwig" />
             <param name="showAdvancedOpt" value="yes" />
             <param name="mode_select" value="scale-regions" />
             <param name="endLabel" value="END" />
@@ -271,7 +265,7 @@
    :alt: Relationship between computeMatrix, heatmapper and profiler
 
 
-You can find more details on the computeMatrix wiki page: https://github.com/fidelram/deepTools/wiki/Visualizations#wiki-computeMatrix
+You can find more details on the computeMatrix doc page: https://deeptools.readthedocs.org/en/release-1.6/content/tools/computeMatrix.html
 
 
 -----
diff -r 28b07293f1ab -r 345a9a2281e0 deepTools_macros.xml
--- a/deepTools_macros.xml	Mon Dec 21 19:10:24 2015 -0500
+++ b/deepTools_macros.xml	Tue Dec 22 13:47:40 2015 -0500
@@ -40,10 +40,10 @@
     </xml>
 
     <token name="@HEATMAP_OPTIONS@">
-        #if $plotting_type.zMin:
+        #if str($plotting_type.zMin) != "":
             --zMin $plotting_type.zMin
         #end if
-        #if $plotting_type.zMax:
+        #if str($plotting_type.zMax) != "":
             --zMax $plotting_type.zMax
         #end if
         --colorMap '$plotting_type.colorMap'
@@ -107,7 +107,11 @@
                     </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)."/>
+                            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])."/>
                     </when>
                     <when value="none" />
                 </conditional>
@@ -408,7 +412,6 @@
             <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>
@@ -456,14 +459,6 @@
     </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 28b07293f1ab -r 345a9a2281e0 static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed