# HG changeset patch
# User bgruening
# Date 1458305318 14400
# Node ID b8741fc443ed4220b620c40103b96f1994bf6de1
# Parent  0b610e3dc97a589618b1a42f4d2f2f1535bac98e
planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 4b6c1004addf9496c85fb8566173e4f9f9e9d356

diff -r 0b610e3dc97a -r b8741fc443ed deepTools_macros.xml
--- a/deepTools_macros.xml	Thu Mar 10 03:23:43 2016 -0500
+++ b/deepTools_macros.xml	Fri Mar 18 08:48:38 2016 -0400
@@ -340,7 +340,7 @@
             ln -s "${bamfile}" "./${counter}.bam" &&
             ln -s "${bamfile.metadata.bam_index}" "./${counter}.bam.bai" &&
             #silent $files.append('%s.bam' % $counter)
-            #silent $labels.append('%s' % ($bamfile.display_name))
+            #silent $labels.append("'%s'" % ($bamfile.display_name))
         #end for
 ]]>
     </token>
@@ -352,7 +352,7 @@
         #for $counter, $bigwig in enumerate($bigwigfiles):
             ln -s "${bigwig}" "${counter}.bw" &&
             #silent $files.append('%s.bw' % $counter)
-            #silent $labels.append('%s' % ($bigwig.display_name))
+            #silent $labels.append("'%s'" % ($bigwig.display_name))
         #end for
 ]]>
     </token>
diff -r 0b610e3dc97a -r b8741fc443ed tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Mar 10 03:23:43 2016 -0500
+++ b/tool_dependencies.xml	Fri Mar 18 08:48:38 2016 -0400
@@ -4,6 +4,6 @@
         <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="deepTools" version="2.2.2">
-        <repository changeset_revision="3349ce2ef9ce" name="package_python_2_7_deeptools_2_2_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="0e67aa094608" name="package_python_2_7_deeptools_2_2_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>
diff -r 0b610e3dc97a -r b8741fc443ed tool_dependencies.xml.orig
--- a/tool_dependencies.xml.orig	Thu Mar 10 03:23:43 2016 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,76 +0,0 @@
-<?xml version='1.0' encoding='utf-8'?>
-<tool_dependency>
-    <package name="numpy" version="1.9">
-        <repository name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" />
-    </package>
-    <package name="pybigwig" version="0.2.4">
-        <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc" prior_installation_required="True"/>
-    </package>
-    <package name="matplotlib" version="1.4">
-        <repository name="package_python_2_7_matplotlib_1_4" owner="iuc" prior_installation_required="True" />
-    </package>
-    <package name="scipy" version="0.14">
-        <repository name="package_python_2_7_scipy_0_14" owner="iuc" prior_installation_required="True" />
-    </package>
-<<<<<<< HEAD
-    <package name="deepTools" version="2.0.1">
-        <repository name="package_python_2_7_deeptools_2_0_1" owner="iuc"/>
-=======
-    <package name="pysam" version="0.8.3">
-        <repository name="package_python_2_7_pysam_0_8_3" owner="iuc" prior_installation_required="True" />
-    </package>
-    <package name="bx-python" version="0.7.2">
-        <repository name="package_python_2_7_bx_python_0_7" owner="iuc" prior_installation_required="True" />
-    </package>
-    <package name="python" version="2.7.10">
-        <repository name="package_python_2_7_10" owner="iuc" prior_installation_required="True" />
->>>>>>> d56067f86089e75354a2fad266002db3730766d9
-    </package>
-    <package name="deepTools" version="2.1.0">
-        <install version="1.0">
-            <actions>
-                <action type="setup_python_environment">
-                    <repository name="package_python_2_7_10" owner="iuc">
-                        <package name="python" version="2.7.10" />
-                    </repository>
-                    <repository name="package_python_2_7_pysam_0_8_3" owner="iuc">
-                        <package name="pysam" version="0.8.3" />
-                    </repository>
-                    <repository name="package_python_2_7_numpy_1_9" owner="iuc">
-                        <package name="numpy" version="1.9" />
-                    </repository>
-                    <repository name="package_python_2_7_matplotlib_1_4" owner="iuc">
-                        <package name="matplotlib" version="1.4" />
-                    </repository>
-                    <repository name="package_python_2_7_scipy_0_14" owner="iuc">
-                        <package name="scipy" version="0.14" />
-                    </repository>
-                    <repository name="package_python_2_7_bx_python_0_7" owner="iuc">
-                        <package name="bx-python" version="0.7.2" />
-                    </repository>
-                    <repository name="package_python_2_7_10_pybigwig_0_2_4" owner="iuc">
-                        <package name="pybigwig" version="0.2.4" />
-                    </repository>
-                    <package sha256sum="3bf835afde02cd5247198db3e01f690899e1fdb86e1821a83ac940d807baa857">https://pypi.python.org/packages/source/d/deepTools/deepTools-2.1.0.tar.gz</package>
-                </action>
-
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="DEEPTOOLS_ROOT_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="DEEPTOOLS_PYTHONPATH" action="set_to">$INSTALL_DIR</environment_variable>
-                    <environment_variable name="DEEPTOOLS_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
-                    <!-- libpng lib path -->
-                    <environment_variable action="set_to" name="LIBPNG_LIB_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
-                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[LIBPNG_LIB_PATH]</environment_variable>
-                    <!-- disable the config file of deepTools -->
-                    <environment_variable name="DEEP_TOOLS_NO_CONFIG" action="set_to">TRUE</environment_variable>
-                </action>
-             </actions>
-         </install>
-         <readme>
-            Installation of deepTools from Fidel Ramirez.
-            https://github.com/fidelram/deepTools
-         </readme>
-     </package>
-</tool_dependency>