# HG changeset patch
# User bgruening
# Date 1535011245 14400
# Node ID fd7e4d6a5d686fef1b934f6dcc3e03b9e76e7fd4
# Parent  c359d704ddee105b6620975e2246f96ada9281d1
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 3024062b63fdc502b46e4f328083493c2274182a

diff -r c359d704ddee -r fd7e4d6a5d68 computeMatrixOperations.xml
--- a/computeMatrixOperations.xml	Thu Apr 05 10:44:01 2018 -0400
+++ b/computeMatrixOperations.xml	Thu Aug 23 04:00:45 2018 -0400
@@ -12,6 +12,15 @@
                 info
                 -m $submodule.matrixFile
                 > $outFileTxt
+            #else if $submodule.command == "relabel":
+                relabel
+                -m $submodule.matrixFile
+                #if $submodule.groupLabels is not None and str($submodule.groupLabels) != '':
+                    --groupLabels $submodule.groupLabels
+                #end if
+                #if $submodule.sampleLabels is not None and str($submodule.sampleLabels) != '':
+                    --sampleLabels $submodule.sampleLabels
+                #end if
             #else if $submodule.command == "subset":
                 subset
                 -m $submodule.matrixFile
@@ -27,6 +36,16 @@
                 -m $submodule.matrixFile
                 --strand $submodule.strand
                 -o $outFileName
+            #else if $submodule.command == "filterValues":
+                filterValues
+                -m $submodule.matrixFile
+                #if $submodule.minValue is not None and str($submodule.minValue) != '':
+                    --min $submodule.minValue
+                #end if
+                #if $submodule.maxValue is not None and str($submodule.maxValue) != '':
+                    --max $submodule.maxValue
+                #end if
+                -o $outFileName
             #else if $submodule.command == "rbind":
                 #set $files=[]
                 #for $f in $submodule.matrixFiles:
@@ -59,8 +78,10 @@
         <conditional name="submodule">
             <param name="command" type="select" label="Operation type">
                 <option value="info" selected="true">Print information (info)</option>
+                <option value="relabel">Relabel the samples and/or groups (relabel)</option>
                 <option value="subset">Subset by samples and/or groups of regions (subset)</option>
                 <option value="filterStrand">Filter by strand (filterStrand)</option>
+                <option value="filterValues">Filter by min/max value (filterValues)</option>
                 <option value="rbind">Bind matrices, top to bottom (rbind)</option>
                 <option value="cbind">Bind matrices, left to right (cbind)</option>
                 <option value="sort">Sort by region order in specified files (sort)</option>
@@ -70,6 +91,15 @@
                        label="Matrix file from the computeMatrix tool" help=""/>
             </when>
 
+            <when value="relabel">
+                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
+                       label="Matrix file from the computeMatrix tool" help=""/>
+                <param argument="groupLabels" type="text" optional="true" label="New Region/Group Labels."
+                    help="If blank, the labels are left unchanged, otherwise they're changed to be those provided here. Multiple labels should be separated by spaces. If you provide labels, you must provide exactly one label for each group of regions."/>
+                <param argument="sampleLabels" type="text" optional="true" label="New Sample Labels."
+                    help="If blank, the labels are left unchanged, otherwise they're changed to be those provided here. Multiple labels should be separated by spaces. If you provide labels, you must provide exactly one label for each sample."/>
+            </when>
+
             <when value="subset">
                 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
                        label="Matrix file from the computeMatrix tool" help=""/>
@@ -82,7 +112,7 @@
             <when value="filterStrand">
                 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
                        label="Matrix file from the computeMatrix tool" help=""/>
-                <param argument="strand" type="select" label="Only include regions on this strand."
+                <param argument="--strand" type="select" label="Only include regions on this strand."
                     help="Only regions on the desired strand will be included in the output. If you desire to instead remove regions on only one strand (or the . strand), separately run this on the other strand and then use the rbind operation.">
                     <option value="+">+</option>
                     <option value="-">-</option>
@@ -90,6 +120,15 @@
                 </param>
             </when>
 
+            <when value="filterValues">
+                <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
+                       label="Matrix file from the computeMatrix tool" help=""/>
+                <param argument="--min" type="float" optional="true" label="Minimum value"
+                       help="Exclude any row in the matrix with a value below this. By default there is no minimum value." />
+                <param argument="--max" type="float" optional="true" label="Maximum value"
+                       help="Exclude any row in the matrix with a value above this. By default there is no maximum value." />
+            </when>
+
             <when value="rbind">
                 <repeat name="matrixFiles" title="Matrix files from computeMatrix" min="2">
                 <param argument="matrixFile" format="deeptools_compute_matrix_archive" type="data"
diff -r c359d704ddee -r fd7e4d6a5d68 deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Apr 05 10:44:01 2018 -0400
+++ b/deepTools_macros.xml	Thu Aug 23 04:00:45 2018 -0400
@@ -1,10 +1,10 @@
 <macros>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">3.0.2</token>
+    <token name="@WRAPPER_VERSION@">3.1.2.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.0.2">deeptools</requirement>
+            <requirement type="package" version="3.1.2">deeptools</requirement>
             <requirement type="package" version="1.7">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -216,7 +216,7 @@
             label="Use a metagene model"
             help="If set and a BED12 or GTF file or files is used to provide regions, only exons will be used. This is convenient for looking at coverage over mature mRNA transcripts or similar uses where introns should be ignored." />
         <param argument="--transcriptID" optional="True" value="transcript" type="text"
-            label="trascript designator"
+            label="transcript designator"
             help="When a GTF file is used to provide regions, only entries with this value as their feature (column 2) will be processed as transcripts. Default: transcript" />
         <param argument="--exonID" optional="True" value="exon" type="text"
             label="exon designator"
@@ -603,6 +603,18 @@
                  (default: False)" />
     </xml>
 
+    <xml name="exactScaling">
+        <param argument="--exactScaling" type="boolean" truevalue="--exactScaling" falsevalue="" checked="False"
+            label="Compute an exact scaling factor"
+            help="Compute an exact scaling factor rather than one based on
+                  sampled reads. This is only useful in cases where you are
+                  filtering some alignments out AND this are both rare and
+                  tend to clump together in the genome. In such cases the
+                  region-based sampling employed by deepTools would produce
+                  inaccurate scaling factors. Note that this option results
+                  in the process taking significantly more time to complete." />
+    </xml>
+
     <xml name="input_save_matrix_values">
         <param argument="--saveMatrix" type="boolean" label="Save the matrix of values underlying the heatmap"/>
     </xml>
@@ -642,7 +654,7 @@
     </xml>
 
     <xml name="output_image_file_format">
-        <data format="png" name="outFileName" label="${tool.name} image">
+        <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
             <change_format>
                 <when input="output.outFileFormat" value="pdf" format="pdf" />
                 <when input="output.outFileFormat" value="svg" format="svg" />
@@ -653,7 +665,7 @@
     </xml>
 
     <xml name="output_image_file_format_not_nested">
-        <data format="png" name="outFileName" label="${tool.name} image">
+        <data format="png" name="outFileName" label="${tool.name} on ${on_string}: Image">
             <change_format>
                 <when input="outFileFormat" value="pdf" format="pdf" />
                 <when input="outFileFormat" value="svg" format="svg" />
diff -r c359d704ddee -r fd7e4d6a5d68 test-data/plotPCA_result1.png
Binary file test-data/plotPCA_result1.png has changed
diff -r c359d704ddee -r fd7e4d6a5d68 test-data/plotPCA_result2.png
Binary file test-data/plotPCA_result2.png has changed