# HG changeset patch
# User bgruening
# Date 1531176926 14400
# Node ID 848ce8f81e6ea424b1d716a41a1aaa3eb390ab71
# Parent  d8c2a68643cec36f8e7ac5556a5ead35d302dfbf
planemo upload for repository https://github.com/deeptools/deepTools/tree/master/galaxy/wrapper/ commit 38cfe39e3b3c82bbc0c2013e3068bd71adc3a9cb

diff -r d8c2a68643ce -r 848ce8f81e6e computeMatrixOperations.xml
--- a/computeMatrixOperations.xml	Thu Apr 05 10:56:44 2018 -0400
+++ b/computeMatrixOperations.xml	Mon Jul 09 18:55:26 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 d8c2a68643ce -r 848ce8f81e6e deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Apr 05 10:56:44 2018 -0400
+++ b/deepTools_macros.xml	Mon Jul 09 18:55:26 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@">3.1.0</token>
     <xml name="requirements">
         <requirements>
-            <requirement type="package" version="3.0.2">deeptools</requirement>
+            <requirement type="package" version="3.1.0">deeptools</requirement>
             <requirement type="package" version="1.7">samtools</requirement>
         </requirements>
         <expand macro="stdio" />
@@ -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>