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comparison rarefaction.shared.xml @ 1:9bdf0bca01c3 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ea40e3d84e7850eb4226d6c85f709dcad18d4ba9
author iuc
date Thu, 18 May 2017 18:12:18 -0400
parents 709508e0cb2d
children 2d1861aaa1d3
comparison
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0:709508e0cb2d 1:9bdf0bca01c3
2 <description>Generate inter-sample rarefaction curves for OTUs</description> 2 <description>Generate inter-sample rarefaction curves for OTUs</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/>
7 <expand macro="version_command"/> 8 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@
11
9 ## create symlinks to input datasets 12 ## create symlinks to input datasets
10 ln -s "$otu" otu.dat && 13 ln -s "$otu" otu.dat &&
11 #if $designc.usedesign == "yes": 14 #if $designc.usedesign == "yes":
12 ln -s "$designc.design" designc.design.dat && 15 ln -s "$designc.design" designc.design.dat &&
13 #end if 16 #end if
40 iters=$iters, 43 iters=$iters,
41 jumble=$jumble 44 jumble=$jumble
42 )' 45 )'
43 | sed 's/ //g' ## mothur trips over whitespace 46 | sed 's/ //g' ## mothur trips over whitespace
44 | mothur 47 | mothur
48 | tee mothur.out.log
45 ]]></command> 49 ]]></command>
46 <inputs> 50 <inputs>
47 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/> 51 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
48 <param name="label" type="select" label="label - OTU Labels" multiple="true"> 52 <param name="label" type="select" label="label - OTU Labels" multiple="true">
49 <expand macro="labeloptions"/> 53 <expand macro="labeloptions"/>
216 <help> 220 <help>
217 <![CDATA[ 221 <![CDATA[
218 222
219 @MOTHUR_OVERVIEW@ 223 @MOTHUR_OVERVIEW@
220 224
221 **Command Documenation** 225 **Command Documentation**
222 226
223 The rarefaction.shared_ command generates inter-sample rarefaction curves using a re-sampling without replacement approach. The traditional way that ecologists use rarefaction is not to randomize the sampling order within a sample, rather between samples. For instance, if we wanted to know the number of OTUs in the human colon, we might sample from various sites within the colon, and sequence a bunch of 16S rRNA genes. By determining the number of OTUs in each sample and comparing the composition of those samples it is possible to determine how well you have sampled the biodiversity within the individual. For calc parameter choices see: http://www.mothur.org/wiki/Calculators 227 The rarefaction.shared_ command generates inter-sample rarefaction curves using a re-sampling without replacement approach. The traditional way that ecologists use rarefaction is not to randomize the sampling order within a sample, rather between samples. For instance, if we wanted to know the number of OTUs in the human colon, we might sample from various sites within the colon, and sequence a bunch of 16S rRNA genes. By determining the number of OTUs in each sample and comparing the composition of those samples it is possible to determine how well you have sampled the biodiversity within the individual. For calc parameter choices see: https://www.mothur.org/wiki/Calculators
224 228
225 .. _rarefaction.shared: http://www.mothur.org/wiki/Rarefaction.shared 229 .. _rarefaction.shared: https://www.mothur.org/wiki/Rarefaction.shared
226 ]]> 230 ]]>
227 </help> 231 </help>
228 <expand macro="citations"/> 232 <expand macro="citations"/>
229 </tool> 233 </tool>