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changeset 2:45ced9c12e18 draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/blob/master/tool_collections/kraken/kraken_report/ commit cb6ebb843c71dcfc73aa05cc616f8e3229170108-dirty
author devteam
date Wed, 15 Jul 2015 15:22:27 -0400
parents bb3d55e8ef3d
children a539aeea69fc
files README.md README.rst kraken-mpa-report.xml kraken-report.xml tool_dependencies.xml
diffstat 5 files changed, 178 insertions(+), 105 deletions(-) [+]
line wrap: on
line diff
--- a/README.md	Tue May 19 16:42:26 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 15:22:27 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.
+
+
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/kraken-mpa-report.xml	Wed Jul 15 15:22:27 2015 -0400
@@ -0,0 +1,71 @@
+<tool id="kraken-mpa-report" name="Kraken-mpa-report" version="1.1.0">
+  <expand macro="version_command" />
+  <expand macro="requirements" />
+  <expand macro="stdio" />
+  <description>
+        view report of classification for multiple samples
+    </description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <command>
+      <![CDATA[
+
+#for $input_count, $input_classification in enumerate( $classification ):
+ ln -s "${input_classification}" "sample_${input_count}" &&
+#end for
+
+kraken-mpa-report @INPUT_DATABASE@
+
+#for $input_count, $input_classification in enumerate( $classification ):
+ "sample_${input_count}"
+#end for
+
+${show_zeros}
+${header_line}
+
+> "$output_report"
+
+
+	]]>
+    </command>
+    <inputs>
+      <param multiple="True" name="classification" type="data" format="tabular" label="Kraken output"/>
+      <param name="show_zeros" type="boolean" truevalue="--show-zeros" falsevalue="" checked="False" label="Display taxa even if they lack a read in any sample" help="--show-zeros"/>
+      <param name="header_line" type="boolean" truevalue="--header-line" falsevalue="" checked="False" label="Display a header line indicating sample IDs" help="--header-line"/>
+        <expand macro="input_database" />
+    </inputs>
+    <outputs>
+        <data format="tabular" name="output_report" />
+    </outputs>
+    <help>
+<![CDATA[
+
+.. class:: warningmark
+
+**Note**: the database used must be the same as the one used in the original Kraken run
+
+-----
+
+**What is Does**
+
+Kraken-mpa-report summarizes read counts across taxonomic ranks for multiple samples. This is convenient for comparing results across multiple expreriments, conditions, locations, etc. It support sthe following parameters::
+
+ --show-zeros    Display taxa even if they lack a read in any sample
+ --header-line   Display a header line indicating sample IDs
+                 (sample IDs are the filenames)
+
+-----
+
+**Output**
+
+The output of kraken-mpa-report is tab-delimited, with one line per taxon.
+
+
+
+
+
+    ]]>
+    </help>
+    <expand macro="citations" />
+</tool>
--- a/kraken-report.xml	Tue May 19 16:42:26 2015 -0400
+++ b/kraken-report.xml	Wed Jul 15 15:22:27 2015 -0400
@@ -1,6 +1,6 @@
-<tool id="kraken-report" name="Kraken-report" version="1.0.0">
+<tool id="kraken-report" name="Kraken-report" version="1.1.0">
     <description>
-        View a sample report of your classification
+        view a sample report of your classification
     </description>
     <macros>
         <import>macros.xml</import>
@@ -12,7 +12,7 @@
         ]]>
     </command>
     <inputs>
-        <param format="tabular" label="Input the Sequenced Kraken Output from your Current History" name="kraken_output" type="data" />
+        <param format="tabular" label="Kraken output" name="kraken_output" type="data" help="Select taxonomy classification produced by kraken"/>
         <expand macro="input_database" />
     </inputs>
     <outputs>
@@ -21,24 +21,22 @@
     <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
 
+-----
 
-**The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows:**
-
-    1)Percentage of reads covered by the clade rooted at this taxon
+**Output**
 
-    2)Number of reads covered by the clade rooted at this taxon
-
-    3)Number of reads assigned directly to this taxon
+The output of kraken-report is tab-delimited, with one line per taxon. The fields of the output, from left-to-right, are as follows::
 
-    4)A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply -.
-
-    5)NCBI taxonomy ID
-
-    6)Indented scientific name
+ 1. Percentage of reads covered by the clade rooted at this taxon
+ 2. Number of reads covered by the clade rooted at this taxon
+ 3. Number of reads assigned directly to this taxon
+ 4. A rank code, indicating (U)nclassified, (D)omain, (K)ingdom, (P)hylum, (C)lass, (O)rder, (F)amily, (G)enus, or (S)pecies. All other ranks are simply filled with a dash.
+ 5. NCBI taxonomy ID
+ 6. Indented scientific name
 
 The scientific names are indented using spaces, according to the tree
 structure specified by the taxonomy.
--- a/tool_dependencies.xml	Tue May 19 16:42:26 2015 -0400
+++ b/tool_dependencies.xml	Wed Jul 15 15:22:27 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>