Mercurial > repos > qfab > rarefaction
changeset 0:ccdc5e9238fc draft
Uploaded
| author | qfab |
|---|---|
| date | Sun, 01 Jun 2014 19:46:00 -0400 |
| parents | |
| children | 6cc245ac2ba9 |
| files | rarefaction/README.txt rarefaction/rarefactionCurve.sh rarefaction/rarefactionCurve.xml rarefaction/repository_dependencies.xml rarefaction/test-data/rarefaction.tabular rarefaction/test-data/reads2otus.rabund rarefaction/tool_dependencies.xml |
| diffstat | 7 files changed, 181 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rarefaction/README.txt Sun Jun 01 19:46:00 2014 -0400 @@ -0,0 +1,36 @@ +Galaxy wrappers for mothurs's Rarefaction Tool +====================================================================== + +The Rarefaction Tool will calculate the intra-sample rarefaction curves +using a re-sampling without replacement approach. + + +Installation +====================================================================== + +Galaxy will automatically install the required dependencies: +- executable mothur (please note for OSX 64-bit mothur 1.30.2 will be +installed, due to issues with the required Readline library and compilers) +- metagenomics datatypes + + +Disclaimer +====================================================================== + +This source code is provided by QFAB Bioinformatics "as is", in the hope +that it will be useful, and any express or implied warranties, including, +but not limited to, the implied warranties of merchantability and fitness +for a particular purpose are disclaimed. +IN NO EVENT SHALL QFAB BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, +SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES HOWEVER CAUSED AND ON ANY +THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT +(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF +THIS SOURCE CODE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +License +====================================================================== + +This work by QFAB Bioinformatics (as part of the GVL project +http://genome.edu.au) is licensed under a Creative Commons +Attribution-NonCommercial-ShareAlike 4.0 International License.
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rarefaction/rarefactionCurve.sh Sun Jun 01 19:46:00 2014 -0400 @@ -0,0 +1,17 @@ +#!/bin/bash + +echo $@ + +filetype=$1 +input=$2 +pctIdent=$3 +label=0$(bc <<< "scale=2; 1-$pctIdent") +output=$4 +pngOutput=$5 + +## use Mothur rarefaction.single to calculate rarefaction +mothur "#rarefaction.single($filetype=$input, label=$label)" 2>1 + +## get filename only remove the extension and copy to galaxy output file +file="${input%.*}" +echo `cp $file.rarefaction $output`
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rarefaction/rarefactionCurve.xml Sun Jun 01 19:46:00 2014 -0400 @@ -0,0 +1,100 @@ +<tool id='rarefaction' name='Rarefaction' version='1.1'> + <description>Calculate and plot rarefaction curves</description> + <requirements> + <requirement type="binary">@BINARY@</requirement> + <requirement type="package" version="1.33.2">mothur</requirement> + </requirements> + <command interpreter="bash"> + rarefactionCurve.sh $ifile.filetype $input $pctIdent $output + </command> + + <inputs> + <conditional name='ifile'> + <param name='filetype' type='select' label='Input file format' + help="Based on the formats used in mothur's rarefaction.single"> + <option value='rabund' selected="true">rabund</option> + <option value='sabund'>sabund</option> + </param> + <when value='rabund'> + <param name='input' type='data' format='rabund' label='OTU list (rabund or sabund format)' + help="The rabund output from the 'Map Reads to OTU' tool."/> + </when> + <when value='sabund'> + <param name='input' type='data' format='sabund' label='OTU list (rabund or sabund format)' + help="File in sabund format used by mothur"/> + </when> + </conditional> + <param name='pctIdent' type='float' value='0.97' label='Minimum identity used in OTU clustering' help='Between 0 - 1.0'/> + </inputs> + + <outputs> + <data name='output' format='tabular' label="${tool.name} on ${on_string}:rarefaction" /> + </outputs> + + <help> +=========== +Description +=========== + +Rarefaction calculation based on mothur_'s rarefaction.single command, which will calculate the intra-sample rarefaction curves using a re-sampling without replacement approach. + +Rarefaction curves provide a way of comparing the richness observed in different samples. Roughly speaking you get the number of OTUs, on average, that you would have been expected to have observed if you hadn't sampled as many individuals. Although a formula exists to generate a rarefaction curve, mothur uses a randomization procedure. It can also help you to assess your sampling intensity. If a rarefaction curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the observed level of richness. Otherwise, you need to keep sampling. Rarefaction is actually a better measure of diversity than it is of richness. + +----- + +---------- +Input +---------- + +OTU list + rabund or sabund format + +---------- +Parameters +---------- + +Input file format + rabund (default) or + sabund + +Minimum identity used in OTU clustering + Used for plot generation + +------ +Output +------ + +(A) Tab delimited file containing the resultes of the rarefaction analysis. The first column 'numsampled' indicates the level of sampling intensity, by default this information is provided every 100 individuals. This would typically be plotted on the x-axis. The second column is the average number of OTUs that were observed for that sampling intensity based on the number of iterations, which is 1000 by default. This would represent the data for the y-axis for the corresponding minimum identity (default 0.03, which corresponds to 97%). The columns 'lci' and 'hci' represent the confidence intervals. + +.. class:: infomark + +Use Galaxy's integrated visualization tool to plot the rarefaction curve. The visualization tool is accessible via the 'Visualize' icon in the extended dataset information area. After having launched the integrated visualization tool select the 'Data Controls' tab. In the 'Data Controls' tab select column 1 (*number sampled*) as 'Data column for X' and use column 2 (*minimum identity*) as 'Data column for Y'. + +------ + +=========== +Resources +=========== + +mothur_ + +.. _mothur: http://www.mothur.org + +**Author** + +Patrick D. Schloss (pschloss@umich.edu) + +**Wrapper Author** + +QFAB Bioinformatics (support@qfab.org) +based on jjohnson mothur_toolsuite wrapper + </help> + <tests> + <test> + <param name="filetype" value="rabund" /> + <param name="input" value="reads2otus.rabund" /> + <param name="pctIdent" value="0.97" /> + <output name="output" file="rarefaction.tabular" ftype="tabular" lines_diff="10" /> + </test> + </tests> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rarefaction/repository_dependencies.xml Sun Jun 01 19:46:00 2014 -0400 @@ -0,0 +1,4 @@ +<?xml version="1.0"?> +<repositories description="This requires the metagenomics datatype definitions (e.g. the rabund format)."> + <repository changeset_revision="ccba8612695e" name="metagenomics_datatypes" owner="qfab" toolshed="http://toolshed.g2.bx.psu.edu/" /> +</repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rarefaction/test-data/rarefaction.tabular Sun Jun 01 19:46:00 2014 -0400 @@ -0,0 +1,16 @@ +numsampled 0.03 lci hci +1 1.0000 1.0000 1.0000 +100 73.0000 65.0000 81.0000 +200 129.0000 118.0000 140.0000 +300 178.0000 165.0000 192.0000 +400 222.0000 208.0000 237.0000 +500 263.0000 248.0000 278.0000 +600 301.0000 285.0000 317.0000 +700 337.0000 321.0000 353.0000 +800 371.0000 354.0000 386.0000 +900 404.0000 389.0000 419.0000 +1000 436.0000 423.0000 449.0000 +1100 467.0000 456.0000 479.0000 +1200 497.0000 488.0000 508.0000 +1300 527.0000 522.0000 532.0000 +1331 536.0000 536.0000 536.0000
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rarefaction/test-data/reads2otus.rabund Sun Jun 01 19:46:00 2014 -0400 @@ -0,0 +1,1 @@ +0.03 536 60 4 3 8 14 1 1 28 2 1 1 17 6 4 1 1 12 7 1 2 7 5 9 1 154 4 1 2 1 7 1 6 1 1 7 7 19 7 1 17 2 2 2 3 4 2 1 4 2 1 7 3 1 5 1 1 3 1 1 2 1 1 1 1 2 10 1 1 1 3 3 11 4 2 1 1 8 4 1 1 20 6 1 1 6 2 7 2 3 28 4 6 6 2 8 10 1 5 4 1 32 1 2 3 1 1 1 13 1 1 1 1 1 1 1 1 2 4 3 2 2 1 1 1 2 6 1 7 4 1 1 1 7 1 3 1 14 1 2 1 1 7 1 5 1 4 2 1 1 1 2 1 1 1 1 1 1 1 2 1 4 1 1 1 1 1 1 1 3 1 1 4 1 1 3 1 1 3 1 1 4 1 1 1 1 1 4 1 1 1 2 2 7 1 2 1 1 1 1 1 1 1 8 2 1 2 1 1 2 1 1 3 2 2 1 3 1 3 1 1 1 1 2 1 1 5 1 1 1 3 1 3 2 2 1 2 2 1 1 1 2 1 2 1 1 4 1 1 1 1 1 1 1 1 2 2 1 2 5 1 1 1 1 3 1 1 1 1 3 1 1 1 1 1 2 1 4 1 1 4 1 2 1 3 1 1 5 1 1 1 1 1 1 1 4 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 4 1 1 2 1 1 1 1 2 1 2 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 7 1 1 1 1 1 1 1 1 1 5 1 1 1 5 2 2 2 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 4 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rarefaction/tool_dependencies.xml Sun Jun 01 19:46:00 2014 -0400 @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="mothur" version="1.30.2-1.33.3"> + <repository changeset_revision="150982d8fd53" name="package_mothur" owner="qfab" toolshed="http://toolshed.g2.bx.psu.edu/" /> + </package> +</tool_dependency> +