# HG changeset patch
# User bgruening
# Date 1450874074 18000
# Node ID 021729469baf6c0ee200ad677f2b25b011d3238d
# Parent  451e73bf38fe72a14058b7f0deaad0b5a89d9af5
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit ae00542731230245927953207977833a0f020b69

diff -r 451e73bf38fe -r 021729469baf computeMatrix.xml
--- a/computeMatrix.xml	Wed Dec 23 04:00:26 2015 -0500
+++ b/computeMatrix.xml	Wed Dec 23 07:34:34 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
@@ -47,8 +41,6 @@
                 --afterRegionStartLength $mode.afterRegionStartLength
             #else
                 --regionBodyLength $mode.regionBodyLength
-                --startLabel "$mode.startLabel"
-                --endLabel "$mode.endLabel"
                 #if $mode.regionStartLength.regionStartLength_select == "yes":
                     --beforeRegionStartLength $mode.regionStartLength.beforeRegionStartLength
                     --afterRegionStartLength $mode.regionStartLength.afterRegionStartLength
@@ -78,19 +70,17 @@
     </command>
     <inputs>
 
-        <repeat name="regionsFiles" title="regions to plot" min="1">
+        <repeat name="regionsFiles" title="Select regions" min="1">
             <param name="regionsFile" format="bed" type="data" label="Regions to plot"
                 help="File, in BED format, containing the regions to plot."/>
-            <param name="label" type="text" size="30" optional="true" value="" label="Label"
-                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"
@@ -100,7 +90,7 @@
                 by the user. Reference-point refers to a position within the BED
                 regions (e.g start of region). In the reference-point mode only
                 those genomic positions before (downstream) and/or after (upstream)
-                the reference point will be plotted.">
+                the reference point will be considered.">
                 <option value="scale-regions" selected="true">scale-regions</option>
                 <option value="reference-point">reference-point</option>
             </param>
@@ -108,14 +98,6 @@
             <when value="scale-regions" >
                 <param argument="--regionBodyLength" type="integer" value="500"
                     label="Distance in bp to which all regions are going to be fitted" help=""/>
-                <param argument="--startLabel" type="text" value="TSS" size="10"
-                    label="Label for the region start"
-                    help ="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 argument="--endLabel" type="text" value="TES" size="10"
-                    label="Label for the region end"
-                    help="Label shown in the plot for the region end. Default is TES (transcription end site)."/>
                 <conditional name="regionStartLength">
                     <param name="regionStartLength_select" type="select" label="Set distance up- and downstream of the given regions">
                         <option value="no" selected="true">no</option>
@@ -186,7 +168,7 @@
                     label="Convert missing values to 0?."
                     help="If set to 'yes', missing values (NAs) are converted to 0.
                           The default is to ignore such cases, which will be
-                          depicted as black areas in the heatmap by default." />
+                          depicted as black areas once a heatmap is created." />
 
                 <expand macro="skipZeros" />
                 <expand macro="skipNAs" />
@@ -214,12 +196,12 @@
         <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 +214,7 @@
         </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 +224,7 @@
         </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 +253,7 @@
    :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 451e73bf38fe -r 021729469baf deepTools_macros.xml
--- a/deepTools_macros.xml	Wed Dec 23 04:00:26 2015 -0500
+++ b/deepTools_macros.xml	Wed Dec 23 07:34:34 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 451e73bf38fe -r 021729469baf static/images/plotCorrelation_galaxy_bw_heatmap_output.png
Binary file static/images/plotCorrelation_galaxy_bw_heatmap_output.png has changed
diff -r 451e73bf38fe -r 021729469baf test-data/bamCoverage_result1.bw
Binary file test-data/bamCoverage_result1.bw has changed
diff -r 451e73bf38fe -r 021729469baf test-data/bamCoverage_result2.bw
Binary file test-data/bamCoverage_result2.bw has changed
diff -r 451e73bf38fe -r 021729469baf test-data/bamCoverage_result3.bg
--- a/test-data/bamCoverage_result3.bg	Wed Dec 23 04:00:26 2015 -0500
+++ b/test-data/bamCoverage_result3.bg	Wed Dec 23 07:34:34 2015 -0500
@@ -5,4 +5,4 @@
 chrM	220	230	7690304.31
 chrM	230	240	6027535.81
 chrM	240	250	3325537.00
-chrM	250	260	623538.19
+chrM	250	16569	623538.2
diff -r 451e73bf38fe -r 021729469baf test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r 451e73bf38fe -r 021729469baf test-data/profiler_result2.png
Binary file test-data/profiler_result2.png has changed