# HG changeset patch
# User devteam
# Date 1436988142 14400
# Node ID 317726be07032142cdb801dac0b8abe95a1e6f0a
# Parent  f093ba52debe646b5932144e28f10e526ffc66e4
planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_filter/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty

diff -r f093ba52debe -r 317726be0703 README.md
--- a/README.md	Tue May 19 16:42:21 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
diff -r f093ba52debe -r 317726be0703 README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Wed Jul 15 15:22:22 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.
+
+
diff -r f093ba52debe -r 317726be0703 kraken-filter.xml
--- a/kraken-filter.xml	Tue May 19 16:42:21 2015 -0400
+++ b/kraken-filter.xml	Wed Jul 15 15:22:22 2015 -0400
@@ -1,6 +1,6 @@
-<tool id="kraken-filter" name="Filter Kraken" version="1.0.0">
+<tool id="kraken-filter" name="Kraken-filter" version="1.1.0">
     <description>
-        by confidence score
+        filter classification by confidence score
     </description>
     <macros>
         <import>macros.xml</import>
@@ -12,8 +12,8 @@
         ]]>
     </command>
     <inputs>
-        <param format="tabular" label="Kraken classified output" name="input" type="data" />
-        <param label="Confidence threshold" max="1" min="0" name="threshold" type="float" value="0" />
+        <param format="tabular" label="Kraken output" name="input" type="data" help="Select taxonomy classification produced by kraken"/>
+        <param label="Confidence threshold" max="1" min="0" name="threshold" type="float" value="0" help="--threshold; A number between 0 and 1; default=0"/>
         <expand macro="input_database" />
     </inputs>
     <outputs>
@@ -22,18 +22,27 @@
     <help>
 <![CDATA[
 
-***Note that the database used must be the same as the one used to generate
-the output file, or the report script may encounter problems.***
+.. class:: warningmark
+
+**Note**: the database used must be the same as the one used in the original Kraken run
 
-A sequence label's score is a fraction C/Q, where C is the number of k-mers mapped to LCA values in the clade rooted at the label, and Q is the number of k-mers in the sequence that lack an ambiguous nucleotide (i.e., they were queried against the database). Consider the example of the LCA mappings in Kraken's output given earlier:
+-----
+
+**What it does**
+
+At present, we have not yet developed a confidence score with a solid probabilistic interpretation for Kraken. However, we have developed a simple scoring scheme that has yielded good results for us, and we've made that available in the kraken-filter script. The approach we use allows a user to specify a threshold score in the [0,1] interval; the ``kraken-filter`` script then will adjust labels up the tree until the label's score (described below) meets or exceeds that threshold. If a label at the root of the taxonomic tree would not have a score exceeding the threshold, the sequence is called unclassified by ``kraken-filter``.
 
-"562:13 561:4 A:31 0:1 562:3" would indicate that:
+A sequence label's score is a fraction C/Q, where C is the number of k-mers mapped to LCA values in the clade rooted at the label, and Q is the number of k-mers in the sequence that lack an ambiguous nucleotide (i.e., they were queried against the database). Consider the example of the LCA mappings in Kraken's output::
+
+ 562:13 561:4 A:31 0:1 562:3 
+
+would indicate that::
 
-    the first 13 k-mers mapped to taxonomy ID #562
-    the next 4 k-mers mapped to taxonomy ID #561
-    the next 31 k-mers contained an ambiguous nucleotide
-    the next k-mer was not in the database
-    the last 3 k-mers mapped to taxonomy ID #562
+ the first 13 k-mers mapped to taxonomy ID #562
+ the next 4 k-mers mapped to taxonomy ID #561
+ the next 31 k-mers contained an ambiguous nucleotide
+ the next k-mer was not in the database
+ the last 3 k-mers mapped to taxonomy ID #562
 
 In this case, ID #561 is the parent node of #562. Here, a label of #562 for this sequence would have a score of C/Q = (13+3)/(13+4+1+3) = 16/21. A label of #561 would have a score of C/Q = (13+4+3)/(13+4+1+3) = 20/21. If a user specified a threshold over 16/21, kraken-filter would adjust the original label from #562 to #561; if the threshold was greater than 20/21, the sequence would become unclassified.
     ]]>
diff -r f093ba52debe -r 317726be0703 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue May 19 16:42:21 2015 -0400
+++ b/tool_dependencies.xml	Wed Jul 15 15:22:22 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>