Mercurial > repos > yhoogstrate > samtools_view_header
changeset 3:257f28d66de8 draft default tip
Uploaded
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
line diff
--- /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>&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>