add missing cote in diffTE.R

l-modolo · Mar 5, 2015 · 1f331a4 · 1f331a4
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Showing 9 changed files with 119 additions and 32 deletions.
diff --git a/PingPong.py b/PingPong.py
@@ -1,21 +1,23 @@
 #!/usr/bin/python3
 # -*-coding:Utf-8 -*
 
-#Copyright (C) 2013 Laurent Modolo
+# Copyright (C) 2015 Laurent Modolo
+
+# This file is part of TEtools suite for galaxy.
 
-#This program is free software; you can redistribute it and/or
-#modify it under the terms of the GNU Lesser General Public
-#License as published by the Free Software Foundation; either
-#version 2.1 of the License, or (at your option) any later version.
+# TEtools is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
 
-#This program is distributed in the hope that it will be useful,
-#but WITHOUT ANY WARRANTY; without even the implied warranty of
-#MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-#Lesser General Public License for more details.
+# TEtools is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+
+# You should have received a copy of the GNU General Public License
+# along with TEtools.  If not, see <http://www.gnu.org/licenses/>.
 
-#You should have received a copy of the GNU Lesser General Public
-#License along with this program; if not, write to the Free Software
-#Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
 
 import argparse
 import configparser

diff --git a/PingPong.xml b/PingPong.xml
@@ -1,3 +1,22 @@
+<!-- 
+    Copyright (C) 2015 Laurent Modolo
+
+    This file is part of TEtools suite for galaxy.
+
+    TEtools is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    TEtools is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with TEtools.  If not, see <http://www.gnu.org/licenses/>.
+-->
+
 <tool id="PingPong" name="PingPong" version="1.0.0" hidden="false">
     <description>PingPong signal analysis</description>
     <version_command interpreter="python3">PingPong.py -v</version_command>

diff --git a/README.md b/README.md
@@ -16,7 +16,7 @@ Then you have to edit the file `galaxy-dist/config/tool_conf.xml` to add the TEt
 <section id="TEtools" name="TEtools">
     <tool file="TEtools/countTE.xml" />
     <tool file="TEtools/diffTE.xml" />
-    <tool file="TEtools/PingPong.xml" />
+    <!-- <tool file="TEtools/PingPong.xml" /> -->
 </section>
 ```
 At least you need to make sure that all the R dependecy for the `diffTE` tool are installed on yout system:

diff --git a/UrQt.xml b/UrQt.xml
@@ -1,3 +1,22 @@
+<!-- 
+    Copyright (C) 2015 Laurent Modolo
+
+    This file is part of TEtools suite for galaxy.
+
+    TEtools is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    TEtools is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with TEtools.  If not, see <http://www.gnu.org/licenses/>.
+-->
+
 <tool id="urqt" name="UrQt" version="1.0.18" hidden="false">
     <description>fastq quality trimming</description>
     <!-- <version_command>UrQt</version_command> -->

diff --git a/countTE.py b/countTE.py
@@ -1,21 +1,22 @@
 #!/usr/bin/python3
 # -*-coding:Utf-8 -*
 
-# Copyright (C) 2013 Laurent Modolo
+# Copyright (C) 2015 Laurent Modolo
+
+# This file is part of TEtools suite for galaxy.
 
-# This program is free software; you can redistribute it and/or
-# modify it under the terms of the GNU Lesser General Public
-# License as published by the Free Software Foundation; either
-# version 2.1 of the License, or (at your option) any later version.
+# TEtools is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
 
-# This program is distributed in the hope that it will be useful,
+# TEtools is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-# Lesser General Public License for more details.
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
 
-# You should have received a copy of the GNU Lesser General Public
-# License along with this program; if not, write to the Free Software
-# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
+# You should have received a copy of the GNU General Public License
+# along with TEtools.  If not, see <http://www.gnu.org/licenses/>.
 
 import argparse
 import configparser

diff --git a/countTE.xml b/countTE.xml
@@ -1,3 +1,21 @@
+<!-- 
+    Copyright (C) 2015 Laurent Modolo
+
+    This file is part of TEtools suite for galaxy.
+
+    TEtools is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    TEtools is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with TEtools.  If not, see <http://www.gnu.org/licenses/>.
+-->
 <tool id="countTE" name="countTE" version="1.0.0" hidden="false">
     <description>fastq quality trimming</description>
     <version_command interpreter="python3">countTE.py -version</version_command>

diff --git a/diffTE.R b/diffTE.R
@@ -1,12 +1,21 @@
 #!/usr/bin/Rscript
 
-# sudo apt-get install libxml2-dev
-# yum install libxml2-devel glibc
-# source("http://bioconductor.org/biocLite.R")
-# biocLite("DESeq2", dep=T)
-# biocLite("gplots", dep=T)
-# biocLite("ggplot2", dep=T)
-# biocLite("RColorBrewer", dep=T)
+# Copyright (C) 2015 Laurent Modolo
+
+# This file is part of TEtools suite for galaxy.
+#
+# TEtools is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# TEtools is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with TEtools.  If not, see <http://www.gnu.org/licenses/>.
 
 args = commandArgs(trailingOnly=FALSE)
 scriptPath <- dirname(sub("--file=","",args[grep("--file",args)]))

diff --git a/diffTE.xml b/diffTE.xml
@@ -1,3 +1,22 @@
+<!--     
+    Copyright (C) 2015 Laurent Modolo
+
+    This file is part of TEtools suite for galaxy.
+
+    TEtools is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    TEtools is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with TEtools.  If not, see <http://www.gnu.org/licenses/>.
+-->
+
 <tool id="diffTE" name="diffTE" version="1.0.0" hidden="false">
     <description>fastq quality trimming</description>
     <version_command interpreter="Rscript">diffTE.R -version=TRUE</version_command>

diff --git a/tool_conf.xml b/tool_conf.xml
@@ -1,5 +1,5 @@
 <section id="TEtools" name="piRNA tools">
     <tool file="TEtools/countTE.xml" />
     <tool file="TEtools/diffTE.xml" />
-    <tool file="TEtools/PingPong.xml" />
+    <!-- <tool file="TEtools/PingPong.xml" /> -->
 </section>