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changeset 2:a080250b8326 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_translate/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
author devteam
date Wed, 15 Jul 2015 15:22:31 -0400
parents f23c90363093
children 443674e0ca7f
files README.md README.rst kraken-translate.xml tool_dependencies.xml
diffstat 4 files changed, 110 insertions(+), 99 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Tue May 19 16:42:30 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,88 +0,0 @@
-Introduction
-============
-
-[Kraken] is a taxonomic sequence classifier that assigns taxonomic
-labels to short DNA reads. It does this by examining the $k$-mers
-within a read and querying a database with those $k$-mers. This database
-contains a mapping of every $k$-mer in [Kraken]'s genomic library to the
-lowest common ancestor (LCA) in a taxonomic tree of all genomes that
-contain that $k$-mer. The set of LCA taxa that correspond to the $k$-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!
-
-[Kraken]:                     http://ccb.jhu.edu/software/kraken/
-[Kraken website]:             http://ccb.jhu.edu/software/kraken/
-[Kraken paper]:               http://genomebiology.com/2014/15/3/R46
-[Kraken GitHub repository]:   https://github.com/DerrickWood/kraken
-
-
-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 $k$-mers; as of Feb. 2015, Kraken's
-    default database contains just under 6 billion (6e9) distinct $k$-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] $k$-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.
-
-[Jellyfish]:  http://www.cbcb.umd.edu/software/jellyfish/
\ No newline at end of file
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Wed Jul 15 15:22:31 2015 -0400
@@ -0,0 +1,92 @@
+Introduction
+============
+
+`Kraken <http://ccb.jhu.edu/software/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 <http://ccb.jhu.edu/software/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 <http://ccb.jhu.edu/software/kraken/>`__ is designed to be
+rapid, sensitive, and highly precise. Our tests on various real and
+simulated data have shown
+`Kraken <http://ccb.jhu.edu/software/kraken/>`__ to have sensitivity
+slightly lower than Megablast with precision being slightly higher. On a
+set of simulated 100 bp reads,
+`Kraken <http://ccb.jhu.edu/software/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 <http://ccb.jhu.edu/software/kraken/>`__, and the latest updates
+to the Kraken source code are available at the `Kraken GitHub
+repository <https://github.com/DerrickWood/kraken>`__.
+
+If you use `Kraken <http://ccb.jhu.edu/software/kraken/>`__ in your
+research, please cite the `Kraken
+paper <http://genomebiology.com/2014/15/3/R46>`__. 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 <http://www.cbcb.umd.edu/software/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.
+
+
--- a/kraken-translate.xml	Tue May 19 16:42:30 2015 -0400
+++ b/kraken-translate.xml	Wed Jul 15 15:22:31 2015 -0400
@@ -1,4 +1,4 @@
-<tool id="kraken-translate" name="Kraken-translate" version="1.0.0">
+<tool id="kraken-translate" name="Kraken-translate" version="1.1.0">
     <description>
         convert taxonomy IDs to names
     </description>
@@ -12,7 +12,7 @@
         ]]>
     </command>
     <inputs>
-        <param format="tabular" label="Kraken classification" name="input" type="data" />
+        <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/>
         <param label="Restrict labels to standard rank assignments" name="mpa_format" truevalue="--mpa-format" falsevalue="" type="boolean" />
         <expand macro="input_database" />
     </inputs>
@@ -21,25 +21,32 @@
     </outputs>
     <help>
         <![CDATA[
+
+.. class:: warningmark
+
+**Note**: the database used must be the same as the one used in the original Kraken run
+
+-------
+
 **What it does**
 
-The file sequences.labels generated by the above example is a text file with two tab-delimited columns, and one line for each classified sequence in sequences.fa; unclassified sequences are not reported by kraken-translate. The first column of kraken-translate's output are the sequence IDs of the classified sequences, and the second column contains the taxonomy of the sequence. For example, an output line from kraken of:
+The file sequences.labels generated by the above example is a text file with two tab-delimited columns, and one line for each classified sequence in sequences.fa; unclassified sequences are not reported by kraken-translate. The first column of kraken-translate's output are the sequence IDs of the classified sequences, and the second column contains the taxonomy of the sequence. For example, an output line from kraken::
 
-C     SEQ1    562     36      562:6
+ C     SEQ1    562     36      562:6
 
-Would result in a corresponding output line from kraken-translate of:
+Would result in a corresponding output line from kraken-translate::
 
-SEQ1  root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli
+ SEQ1  root;cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacteriales;Enterobacteriaceae;Escherichia;Escherichia coli
 
-Alternatively, kraken-translate accepts the option --mpa-format which will report only levels of the taxonomy with standard rank assignments (superkingdom, kingdom, phylum, class, order, family, genus, species), and uses pipes to delimit the various levels of the taxonomy. For example, kraken-translate --mpa-format --db $DBNAME with the above example output from kraken would result in the following line of output:
+Alternatively, kraken-translate accepts the option ``--mpa-format`` which will report only levels of the taxonomy with standard rank assignments (superkingdom, kingdom, phylum, class, order, family, genus, species), and uses pipes to delimit the various levels of the taxonomy. For example, ``kraken-translate --mpa-format`` with the above example output from kraken would result in the following line of output::
 
-SEQ1  d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli
+ SEQ1  d__Bacteria|p__Proteobacteria|c__Gammaproteobacteria|o__Enterobacteriales|f__Enterobacteriaceae|g__Escherichia|s__Escherichia_coli
 
-Taxonomy assignments above the superkingdom (d__) rank are represented as just "root" when using the --mpa-report option with kraken-translate.
+Taxonomy assignments above the superkingdom rank are represented as just "root" when using the ``--mpa-report`` option with kraken-translate.
         ]]>
     </help>
     <expand macro="requirements" />
     <expand macro="stdio" />
     <expand macro="version_command" />
     <expand macro="citations" />
-</tool>
\ No newline at end of file
+</tool>
--- a/tool_dependencies.xml	Tue May 19 16:42:30 2015 -0400
+++ b/tool_dependencies.xml	Wed Jul 15 15:22:31 2015 -0400
@@ -1,6 +1,6 @@
 <?xml version="1.0"?>
 <tool_dependency>
   <package name="kraken" version="0.10.5">
-      <repository changeset_revision="e79fee8f87fa" name="package_kraken_0_10_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+      <repository changeset_revision="3525db901c16" name="package_kraken_0_10_5" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>