Mercurial > repos > yhoogstrate > samtools_view_header

changeset 3:257f28d66de8 draft default tip

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author yhoogstrate
date Thu, 20 Nov 2014 03:55:28 -0500
parents 1a77794c72ed
children
files README.rst samtools_view_header.xml tool_dependencies.xml
diffstat 3 files changed, 100 insertions(+), 7 deletions(-) [+]
line wrap: on
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Thu Nov 20 03:55:28 2014 -0500
@@ -0,0 +1,80 @@
+Samtools (view -H) wrapper for Galaxy
+=====================================
+
+http://samtools.sourceforge.net/
+
+Quickly show the header lines of a SAM / BAM file.
+
+Development
+-----------
+
+* Repository-Maintainer: Youri Hoogstrate
+
+* Repository-Development: https://bitbucket.org/EMCbioinf/galaxy-tool-shed-tools
+
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
+http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
+
+More tools by the Translational Research IT (TraIT) project can be found in the following repository:
+
+http://toolshed.dtls.nl/
+
+License
+-------
+
+**samtools**:
+
+MIT/Expat License: https://raw.githubusercontent.com/samtools/samtools/develop/LICENSE
+
+    The MIT/Expat License
+
+    Copyright (C) 2008-2014 Genome Research Ltd.
+
+    Permission is hereby granted, free of charge, to any person obtaining a copy
+    of this software and associated documentation files (the "Software"), to deal
+    in the Software without restriction, including without limitation the rights
+    to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+    copies of the Software, and to permit persons to whom the Software is
+    furnished to do so, subject to the following conditions:
+
+    The above copyright notice and this permission notice shall be included in
+    all copies or substantial portions of the Software.
+
+    THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+    IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+    FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
+    THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+    LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+    FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+    DEALINGS IN THE SOFTWARE.
+
+    [The use of a range of years within a copyright notice in this distribution
+    should be interpreted as being equivalent to a list of years including the
+    first and last year specified and all consecutive years between them.
+
+    For example, a copyright notice that reads "Copyright (C) 2005, 2007-2009,
+    2011-2012" should be interpreted as being identical to a notice that reads
+    "Copyright (C) 2005, 2007, 2008, 2009, 2011, 2012" and a copyright notice
+    that reads "Copyright (C) 2005-2012" should be interpreted as being identical
+    to a notice that reads "Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010,
+    2011, 2012".]
+
+**This wrapper**:
+
+    Copyright (C) 2013-2014  Youri Hoogstrate
+
+    This program 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 General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <http://www.gnu.org/licenses/>.
--- a/samtools_view_header.xml	Wed Jun 11 08:34:22 2014 -0400
+++ b/samtools_view_header.xml	Thu Nov 20 03:55:28 2014 -0500
@@ -1,10 +1,13 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<tool id="samtools_view_header" name="Samtools view header">
+<tool id="samtools_view_header" name="Samtools view header" version="0.1.19.a">
 	<description>Show only the header of a BAM or SAM file using samtools.</description>
 	<requirements>
 		<requirement type="package" version="5.9">ncurses</requirement>
 		<requirement type="package" version="0.1.19">samtools</requirement>
 	</requirements>
+	
+	<version_command>samtools 2&gt;&amp;1 | grep -i "version:"</version_command>
+	
 	<command>
 		samtools
 			 view 
@@ -46,12 +49,22 @@
 
 * samtools: MIT License
 
-**Contact**
+Contact
+-------
 
-The tool wrapper has been written by Youri Hoogstrate from the Erasmus Medical Center (Rotterdam, Netherlands) on behalf of the Translational Research IT (TraIT) project:
+The tool wrapper has been written by Youri Hoogstrate from the Erasmus
+Medical Center (Rotterdam, Netherlands) on behalf of the Translational
+Research IT (TraIT) project:
+
 http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch
 
-More tools by the Translational Research IT (TraIT) project can be found in the following repository:
+More tools by the Translational Research IT (TraIT) project can be found
+in the following toolsheds:
+
 http://toolshed.dtls.nl/
+
+http://toolshed.g2.bx.psu.edu
+
+http://testtoolshed.g2.bx.psu.edu/
 </help>
 </tool>
\ No newline at end of file
--- a/tool_dependencies.xml	Wed Jun 11 08:34:22 2014 -0400
+++ b/tool_dependencies.xml	Thu Nov 20 03:55:28 2014 -0500
@@ -1,10 +1,10 @@
 <?xml version="1.0"?>
 <tool_dependency>
 	<package name="ncurses" version="5.9">
-		<repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+		<repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 	</package>
 		
 	<package name="samtools" version="0.1.19">
-		<repository changeset_revision="40250a414486" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+		<repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
 	</package>
-</tool_dependency>
\ No newline at end of file
+</tool_dependency>