Mercurial > repos > iuc > vegan_rarefaction

comparison vegan_rarefaction.xml @ 4:c9dac54e8039 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author iuc
date Fri, 07 Sep 2018 10:56:52 -0400
parents 2d2a742708c4
children
comparison
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3:2d2a742708c4 4:c9dac54e8039
1 <tool id="vegan_rarefaction" name="Vegan Rarefaction" version="0.0.3"> 1 <tool id="vegan_rarefaction" name="Vegan Rarefaction" version="@TOOL_VERSION@">
2 <description> 2 <description>
3 curve and statistics 3 curve and statistics
4 </description> 4 </description>
5 <macros> 5 <macros>
6 <import>vegan_macros.xml</import> 6 <import>macros.xml</import>
7 </macros> 7 </macros>
8 <expand macro="requirements" /> 8 <expand macro="requirements" />
9 <expand macro="stdio" /> 9 <expand macro="stdio" />
10 <expand macro="version_command" /> 10 <expand macro="version_command" />
11 <command><![CDATA[ 11 <command><![CDATA[
125 <output name="output_slope" ftype="tabular" file="vegan_output_slope.tabular" /> 125 <output name="output_slope" ftype="tabular" file="vegan_output_slope.tabular" />
126 </test> 126 </test>
127 </tests> 127 </tests>
128 <help> 128 <help>
129 <![CDATA[ 129 <![CDATA[
130 130
131 Gives the expected species richness in random subsamples of size sample from the community. The size of sample should be smaller than total community size, but the function will work for larger sample as well (with a warning) and return non-rarefied species richness (and standard error = 0). Rarefaction can be performed only with genuine counts of individuals. The function rarefy is based on Hurlbert’s (1971) formulation, and the standard errors on Heck et al. (1975). 131 Gives the expected species richness in random subsamples of size sample from the community. The size of sample should be smaller than total community size, but the function will work for larger sample as well (with a warning) and return non-rarefied species richness (and standard error = 0). Rarefaction can be performed only with genuine counts of individuals. The function rarefy is based on Hurlbert’s (1971) formulation, and the standard errors on Heck et al. (1975).
132 132
133 Returns probabilities that species occur in a rarefied community of size sample. 133 Returns probabilities that species occur in a rarefied community of size sample.
134 134
135 Draws a rarefaction curve for each row of the input data. The rarefaction curves are evaluated using the interval of step sample sizes, always including 1 and total sample size. If sample is specified, a vertical line is drawn at sample with horizontal lines for the rarefied species richnesses. 135 Draws a rarefaction curve for each row of the input data. The rarefaction curves are evaluated using the interval of step sample sizes, always including 1 and total sample size. If sample is specified, a vertical line is drawn at sample with horizontal lines for the rarefied species richnesses.
136 136
137 137
138 .. class:: warningmark 138 .. class:: warningmark
139 139