Mercurial > repos > iuc > mothur_cooccurrence

comparison cooccurrence.xml @ 1:72f9b9aca28d 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 18:23:54 -0400
parents e1330cc9b7e9
children 1bebb226e793
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0:e1330cc9b7e9 1:72f9b9aca28d
2 <description>tests whether presence-absence patterns differ from chance</description> 2 <description>tests whether presence-absence patterns differ from chance</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 14
12 echo 'cooccurrence( 15 echo 'cooccurrence(
13 shared=otu.dat, 16 shared=otu.dat,
21 ,groups=${ str($groups).replace(",","-") } 24 ,groups=${ str($groups).replace(",","-") }
22 #end if 25 #end if
23 )' 26 )'
24 | sed 's/ //g' ## mothur trips over whitespace 27 | sed 's/ //g' ## mothur trips over whitespace
25 | mothur 28 | mothur
29 | tee mothur.out.log
26 ]]></command> 30 ]]></command>
27 <inputs> 31 <inputs>
28 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/> 32 <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared file"/>
29 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/> 33 <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
30 <param name="metric" type="select" label="metric - test metric for scoring"> 34 <param name="metric" type="select" label="metric - test metric for scoring">
89 <help> 93 <help>
90 <![CDATA[ 94 <![CDATA[
91 95
92 @MOTHUR_OVERVIEW@ 96 @MOTHUR_OVERVIEW@
93 97
94 **Command Documenation** 98 **Command Documentation**
95 99
96 The cooccurrence_ command variance calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance. The input is a shared_ file. The output can be filtered by groups and labels. 100 The cooccurrence_ command variance calculates four metrics and tests their significance to assess whether presence-absence patterns are different than what one would expect by chance. The input is a shared_ file. The output can be filtered by groups and labels.
97 101
98 102
99 103
152 The default values of cscore and sim2 have been selected because the c-score is not very sensitive to noise in the data and when used with sim9 or sim2 is not particularly prone to false positives. Sim2 has been chosen because of the prevalence of degenerate matrices. These are just guidelines, however, be sure to select a metric and matrix model that is best suited to the type of data you are analyzing. 156 The default values of cscore and sim2 have been selected because the c-score is not very sensitive to noise in the data and when used with sim9 or sim2 is not particularly prone to false positives. Sim2 has been chosen because of the prevalence of degenerate matrices. These are just guidelines, however, be sure to select a metric and matrix model that is best suited to the type of data you are analyzing.
153 It should be noted that sim9 cannot be used with vratio because in sim9 both the column and row totals are maintained, hence there will be no variance. 157 It should be noted that sim9 cannot be used with vratio because in sim9 both the column and row totals are maintained, hence there will be no variance.
154 Please see [5] for more details on metric/null model selection. 158 Please see [5] for more details on metric/null model selection.
155 159
156 160
157 .. _shared: http://www.mothur.org/wiki/Shared_file 161 .. _shared: https://www.mothur.org/wiki/Shared_file
158 .. _cooccurrence: http://www.mothur.org/wiki/Cooccurrence 162 .. _cooccurrence: https://www.mothur.org/wiki/Cooccurrence
159 163
160 v1.26.0: Updated to Mothur 1.33 164 v1.26.0: Updated to Mothur 1.33
161 ]]> 165 ]]>
162 </help> 166 </help>
163 <expand macro="citations"/> 167 <expand macro="citations"/>