Repository 'fastq_mcf'
http://toolshed.g2.bx.psu.edu/view/jjohnson/fastq_mcf
fastq_mcf
unrestricted
FastqMcf from ea-utils: remove barcodes and primers,filter and clip
http://code.google.com/p/ea-utils/wiki/FastqMcf

fastq-mcf attempts to:

Detect X remove sequencing adapters and primers
Detect limited skewing at the ends of reads and clip
Detect poor quality at the ends of reads and clip
Detect N's, and remove from ends
Remove reads with CASAVA 'Y' flag (purity filtering)
Discard sequences that are too short after all of the above
Keep multiple mate-reads in sync while doing all of the above
1:b61f1466ce8f
jjohnson
True
181

Repository README files - may contain important installation or license information


== ea-utils Galaxy Wrapper ==

This is a Galaxy wrapper for some ea-utils tools, fastq-join and sam-stats.

** Installation **

Installation from a tool shed provides the necessary tool dependencies.

Otherwise, make sure fastq-join and sam-stats are in the path.
Move the test data files to your galaxy root test-data.
Move the xml files to a subdirectory of your tools directory and add lines in tool_conf.xml to point to them.
Restart the Galaxy server.

** Attribution **

The ea-utils package and associated documentation can be found at: http://code.google.com/p/ea-utils/


Dependencies of this repository

Name Version Type
ea-utils 1.1.2-484 package

Contents of this repository

Name Description Version
FastqMcf sequence quality filtering and clipping 1.0

Automated tool test results

Time tested: 2014-04-23 06:52:06
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13181:7a7985a007fb
Galaxy database version: 118
Tool shed revision: 13123:e6876f691854
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: fastq_mcf
Tool version: fastq_mcf
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/fastq_mcf/fastq_mcf/1.0)
TypeNameVersion
ea-utils package 1.1.2-484
Installation directory
/ToolDepsMain/ea-utils/1.1.2-484/jjohnson/fastq_mcf/b61f1466ce8f
Time tested: 2014-04-17 04:56:11
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13085:c05752549163
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: fastq_mcf
Tool version: fastq_mcf
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/fastq_mcf/fastq_mcf/1.0)
TypeNameVersion
ea-utils package 1.1.2-484
Installation directory
/ToolDepsMain/ea-utils/1.1.2-484/jjohnson/fastq_mcf/b61f1466ce8f
Time tested: 2014-04-16 04:50:22
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13065:1ad62c772728
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: fastq_mcf
Tool version: fastq_mcf
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/fastq_mcf/fastq_mcf/1.0)
TypeNameVersion
ea-utils package 1.1.2-484
Installation directory
/ToolDepsMain/ea-utils/1.1.2-484/jjohnson/fastq_mcf/b61f1466ce8f
Time tested: 2014-04-15 05:23:30
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 13058:1165a5a1221a
Galaxy database version: 118
Tool shed revision: 12961:888478c66456
Tool shed database version: 22
Tool shed mercurial version: 2.2.3
Tool id: fastq_mcf
Tool version: fastq_mcf
Test: test_tool_000000 (functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/jjohnson/fastq_mcf/fastq_mcf/1.0)
TypeNameVersion
ea-utils package 1.1.2-484
Installation directory
/ToolDepsMain/ea-utils/1.1.2-484/jjohnson/fastq_mcf/b61f1466ce8f

Categories
Sequence Analysis
Fasta Manipulation