# HG changeset patch
# User devteam
# Date 1437663360 14400
# Node ID cbb802a726fd998ae269262e0a29e0838a752409
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
diff -r 000000000000 -r cbb802a726fd README.rst
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst Thu Jul 23 10:56:00 2015 -0400
@@ -0,0 +1,92 @@
+Introduction
+============
+
+`Kraken `__ is a taxonomic sequence
+classifier that assigns taxonomic labels to short DNA reads. It does
+this by examining the :math:`k`-mers within a read and querying a
+database with those :math:`k`-mers. This database contains a mapping of
+every :math:`k`-mer in
+`Kraken `__'s genomic library to
+the lowest common ancestor (LCA) in a taxonomic tree of all genomes that
+contain that :math:`k`-mer. The set of LCA taxa that correspond to the
+:math:`k`-mers in a read are then analyzed to create a single taxonomic
+label for the read; this label can be any of the nodes in the taxonomic
+tree. `Kraken `__ is designed to be
+rapid, sensitive, and highly precise. Our tests on various real and
+simulated data have shown
+`Kraken `__ to have sensitivity
+slightly lower than Megablast with precision being slightly higher. On a
+set of simulated 100 bp reads,
+`Kraken `__ processed over 1.3
+million reads per minute on a single core in normal operation, and over
+4.1 million reads per minute in quick operation.
+
+The latest released version of Kraken will be available at the `Kraken
+website `__, and the latest updates
+to the Kraken source code are available at the `Kraken GitHub
+repository `__.
+
+If you use `Kraken `__ in your
+research, please cite the `Kraken
+paper `__. Thank you!
+
+System Requirements
+===================
+
+Note: Users concerned about the disk or memory requirements should read
+the paragraph about MiniKraken, below.
+
+- **Disk space**: Construction of Kraken's standard database will
+ require at least 160 GB of disk space. Customized databases may
+ require more or less space. Disk space used is linearly proportional
+ to the number of distinct :math:`k`-mers; as of Feb. 2015, Kraken's
+ default database contains just under 6 billion (6e9) distinct
+ :math:`k`-mers.
+
+ In addition, the disk used to store the database should be
+ locally-attached storage. Storing the database on a network
+ filesystem (NFS) partition can cause Kraken's operation to be very
+ slow, or to be stopped completely. As NFS accesses are much slower
+ than local disk accesses, both preloading and database building will
+ be slowed by use of NFS.
+
+- **Memory**: To run efficiently, Kraken requires enough free memory to
+ hold the database in RAM. While this can be accomplished using a
+ ramdisk, Kraken supplies a utility for loading the database into RAM
+ via the OS cache. The default database size is 75 GB (as of Feb.
+ 2015), and so you will need at least that much RAM if you want to
+ build or run with the default database.
+
+- **Dependencies**: Kraken currently makes extensive use of Linux
+ utilities such as sed, find, and wget. Many scripts are written using
+ the Bash shell, and the main scripts are written using Perl. Core
+ programs needed to build the database and run the classifier are
+ written in C++, and need to be compiled using g++. Multithreading is
+ handled using OpenMP. Downloads of NCBI data are performed by wget
+ and in some cases, by rsync. Most Linux systems that have any sort of
+ development package installed will have all of the above listed
+ programs and libraries available.
+
+ Finally, if you want to build your own database, you will need to
+ install the
+ `Jellyfish `__
+ :math:`k`-mer counter. Note that Kraken only supports use of
+ Jellyfish version 1. Jellyfish version 2 is not yet compatible with
+ Kraken.
+
+- **Network connectivity**: Kraken's standard database build and
+ download commands expect unfettered FTP and rsync access to the NCBI
+ FTP server. If you're working behind a proxy, you may need to set
+ certain environment variables (such as ``ftp_proxy`` or
+ ``RSYNC_PROXY``) in order to get these commands to work properly.
+
+- **MiniKraken**: To allow users with low-memory computing environments
+ to use Kraken, we supply a reduced standard database that can be
+ downloaded from the Kraken web site. When Kraken is run with a
+ reduced database, we call it MiniKraken.
+
+ The database we make available is only 4 GB in size, and should run
+ well on computers with as little as 8 GB of RAM. Disk space required
+ for this database is also only 4 GB.
+
+
diff -r 000000000000 -r cbb802a726fd kraken-filter.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/kraken-filter.xml Thu Jul 23 10:56:00 2015 -0400
@@ -0,0 +1,54 @@
+
+
+ filter classification by confidence score
+
+
+ macros.xml
+
+
+ "$filtered_output"
+ ]]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
diff -r 000000000000 -r cbb802a726fd macros.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/macros.xml Thu Jul 23 10:56:00 2015 -0400
@@ -0,0 +1,30 @@
+
+
+
+
+ kraken
+
+
+
+
+
+
+
+
+ export LC_ALL=C && kraken --version
+
+
+
+
+
+
+
+
+
+
+ 10.1186/gb-2014-15-3-r46
+
+
+ --db ${kraken_database.fields.name}
+ export KRAKEN_DB_PATH="${kraken_database.fields.path}"
+
\ No newline at end of file
diff -r 000000000000 -r cbb802a726fd tool-data/kraken_databases.loc.sample
diff -r 000000000000 -r cbb802a726fd tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Jul 23 10:56:00 2015 -0400
@@ -0,0 +1,8 @@
+
+
+
+
+
diff -r 000000000000 -r cbb802a726fd tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Jul 23 10:56:00 2015 -0400
@@ -0,0 +1,6 @@
+
+
+
+
+
+