# HG changeset patch
# User bgruening
# Date 1485248337 18000
# Node ID af9d00228156b52d65e248e588ac6f07bd700c28
# Parent  470e6a076c80a38375d9363c0d42a2cc10846c45
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 999ec5d9b5882702497d8117a7d26536a67e19ca

diff -r 470e6a076c80 -r af9d00228156 bigwigCompare.xml
--- a/bigwigCompare.xml	Mon Dec 05 07:48:06 2016 -0500
+++ b/bigwigCompare.xml	Tue Jan 24 03:58:57 2017 -0500
@@ -49,15 +49,16 @@
                 help="The default is to output the log2ratio between the two samples.
                 The reciprocal ratio returns the negative of the inverse of the ratio if
                 the ratio is less than 0. The resulting values are interpreted as negative
-                fold changes. To output the scaled values from the first or second BAM file,
+                fold changes. To output the scaled values from the first or second bigWig file,
                 select 'first' or 'second'.">
-                <option value="log2" selected="true">Compute log2 of the number of reads ratio</option>
-                <option value="ratio">Compute the ratio of the number of reads</option>
-                <option value="subtract">Compute difference (subtract input from treatment) of the number of reads</option>
-                <option value="add">Compute the sum of number of reads</option>
+                <option value="log2" selected="true">Compute log2 of the signal ratio</option>
+                <option value="ratio">Compute the ratio signals</option>
+                <option value="subtract">Compute difference (subtract input from treatment) of the signal</option>
+                <option value="add">Compute the sum of the signals</option>
+                <option value="mean">Compute the mean of the signal in the two files</option>
                 <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
-                <option value="first">Returns the scaled value of the first BAM file</option>
-                <option value="second">Returns the scaled value of the second BAM file</option>
+                <option value="first">Returns the scaled value of the first bigWig file</option>
+                <option value="second">Returns the scaled value of the second bigWig file</option>
             </param>
             <when value="log2">
                 <expand macro="pseudocount" />
@@ -67,6 +68,7 @@
             </when>
             <when value="subtract" />
             <when value="add" />
+            <when value="mean" />
             <when value="first" />
             <when value="second" />
             <when value="reciprocal_ratio">
diff -r 470e6a076c80 -r af9d00228156 deepTools_macros.xml
--- a/deepTools_macros.xml	Mon Dec 05 07:48:06 2016 -0500
+++ b/deepTools_macros.xml	Tue Jan 24 03:58:57 2017 -0500
@@ -98,11 +98,11 @@
     </xml>
 
     <token name="@THREADS@">--numberOfProcessors "\${GALAXY_SLOTS:-4}"</token>
-    <token name="@WRAPPER_VERSION@">2.4.1</token>
+    <token name="@WRAPPER_VERSION@">2.4.2</token>
     <xml name="requirements">
         <requirements>
             <requirement type="package" version="2.7.10">python</requirement>
-            <requirement type="package" version="2.4.1">deeptools</requirement>
+            <requirement type="package" version="2.4.2">deeptools</requirement>
             <yield />
         </requirements>
         <expand macro="stdio" />
@@ -299,7 +299,7 @@
         <param argument="--sortRegions" type="select" label="Sort regions"
             help="Whether the heatmap should present the regions sorted. The default is to sort in descending order based on the mean value per region.">
             <option value="no">no ordering</option>
-            <option value="descend">descending order</option>
+            <option value="descend" selected="true">descending order</option>
             <option value="ascend">ascending order</option>
         </param>
     </xml>
@@ -450,10 +450,10 @@
             #end for
         #else:
             #for $counter, $f in enumerate($multibam_conditional.multibam_repeats):
-                ln -s "${f.bamfile}" "./${counter}.bam" &&
-                ln -s "${f.bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
+                ln -s "${f.bamfiles}" "./${counter}.bam" &&
+                ln -s "${f.bamfiles.metadata.bam_index}" "./${counter}.bam.bai" &&
                 #silent $files.append('%s.bam' % $counter)
-                #silent $labels.append("'%s'" % ($f.bamfile.display_name))
+                #silent $labels.append("'%s'" % ($f.bamfiles.display_name))
             #end for
         #end if
 ]]>
@@ -471,9 +471,9 @@
             #end for
         #else:
             #for $counter, $f in enumerate($multibigwig_conditional.multibigwig_repeats):
-                ln -s "${f.bigwig}" "${counter}.bw" &&
+                ln -s "${f.bigwigfiles}" "${counter}.bw" &&
                 #silent $files.append('%s.bw' % $counter)
-                #silent $labels.append("'%s'" % ($f.bigwig.display_name))
+                #silent $labels.append("'%s'" % ($f.bigwigfiles.display_name))
             #end for
         #end if
 ]]>
diff -r 470e6a076c80 -r af9d00228156 repository_dependencies.xml
--- a/repository_dependencies.xml	Mon Dec 05 07:48:06 2016 -0500
+++ b/repository_dependencies.xml	Tue Jan 24 03:58:57 2017 -0500
@@ -1,4 +1,4 @@
 <?xml version="1.0"?>
 <repositories>
-    <repository changeset_revision="26e3ae5f74ed" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <repository changeset_revision="298d15849a14" name="data_manager_twobit_builder" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 </repositories>
diff -r 470e6a076c80 -r af9d00228156 tool_dependencies.xml
--- a/tool_dependencies.xml	Mon Dec 05 07:48:06 2016 -0500
+++ b/tool_dependencies.xml	Tue Jan 24 03:58:57 2017 -0500
@@ -3,7 +3,7 @@
     <package name="python" version="2.7.10">
         <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
-    <package name="deeptools" version="2.4.1">
-        <repository changeset_revision="939327bd44e7" name="package_python_2_7_deeptools_2_4_1" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    <package name="deeptools" version="2.4.2">
+        <repository changeset_revision="13e8eb777151" name="package_python_2_7_deeptools_2_4_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>