Mercurial > repos > iuc > vegan_rarefaction

annotate vegan_rarefaction.xml @ 2:b0d5976540e3 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
author iuc
date Fri, 07 Sep 2018 11:31:02 -0400
parents dd2705a31239
children af1211ed6c8e
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
b0d5976540e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 1
diff changeset
1 <tool id="vegan_rarefaction" name="Vegan Rarefaction" version="@TOOL_VERSION@">
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
2 <description>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
3 curve and statistics
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
4 </description>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
5 <macros>
2
b0d5976540e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 1
diff changeset
6 <import>macros.xml</import>
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
7 </macros>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
8 <expand macro="requirements" />
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
9 <expand macro="stdio" />
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
10 <expand macro="version_command" />
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
11 <command><![CDATA[
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
12 #if "output_r_script" in str( $include_outputs ).split( "," ):
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
13 cp "${vegan_rarefaction_script}" "${output_r_script}" &&
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
14 #end if
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
15 Rscript "${vegan_rarefaction_script}"
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
16 ]]>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
17 </command>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
18 <configfiles>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
19 <configfile name="vegan_rarefaction_script"><![CDATA[
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
20 @RSCRIPT_PREAMBLE@
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
21 @RSCRIPT_LOAD_TABULAR_FILE@
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
22 #set $include_files = str( $include_outputs ).split( "," )
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
23
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
24 #if str( $sample_size ) == '':
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
25 raremax <- min(rowSums(input_abundance))
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
26 raremax_offset <- -1
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
27 sprintf("Automatically determining subsampling size, will apply offset to slope calculation and species probabilities.")
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
28 #else:
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
29 raremax = $sample_size
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
30 raremax_offset <- 0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
31 #end if
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
32 sprintf("Using sample size: %i", raremax)
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
33 Srare <- rarefy(input_abundance, sample=raremax, se=FALSE, MARGIN=1)
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
34 #if "output_richness" in $include_files:
1
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
35 write.table(Srare, "${output_richness}", quote=FALSE, col.names=NA, sep = "\t")
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
36 #end if
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
37
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
38 #if "output_slope" in $include_files:
1
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
39 write.table(rareslope(input_abundance, sample=raremax+raremax_offset), "${output_slope}", quote=FALSE, sep = "\t")
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
40 #end if
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
41
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
42 S <- specnumber(input_abundance)
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
43 #if "output_species_count" in $include_files:
1
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
44 write.table(S, "${ output_species_count }", quote=FALSE, col.names=NA, sep="\t" )
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
45 #end if
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
46
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
47 #if "output_species_frequency" in $include_files:
1
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
48 write.table(specnumber(input_abundance, MARGIN=2), "${ output_species_frequency }", quote=FALSE, col.names=NA, sep="\t" )
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
49 #end if
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
50
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
51 #if "output_species_probabilities" in $include_files:
1
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
52 write.table(drarefy(input_abundance, sample=raremax+raremax_offset), "${ output_species_probabilities }", quote=FALSE, col.names=NA, sep="\t" )
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
53 #end if
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
54
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
55 #if "output_random_rarefied" in $include_files:
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
56 write.table( t( rrarefy(input_abundance, sample=raremax) ), "${ output_random_rarefied }", quote=FALSE, col.names=NA, sep="\t" )
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
57 #end if
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
58
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
59 #if "output_plot" in $include_files:
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
60 png('${output_plot}', width=1020, height=800, units='px')
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
61 rarecurve(input_abundance, step = ${step_size}, sample = raremax, xlab = "${xlab}", ylab = "${ylab}", label="${label}", col = "blue", cex = 0.6)
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
62 invisible(dev.off())
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
63 #end if
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
64 ]]>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
65 </configfile>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
66 </configfiles>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
67 <inputs>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
68 <expand macro="params_load_tabular_file" />
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
69 <param name="sample_size" type="integer" value="" min="1" optional="True" label="Subsample size for rarefying community" help="Leave empty to subsample by community size for the smallest sample."/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
70 <param name="step_size" type="integer" value="1" min="1" label="Step size for sample sizes"/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
71 <param name="xlab" type="text" value="Sample Size" label="X-axis label"/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
72 <param name="ylab" type="text" value="Species" label="Y-axis label"/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
73 <param name="label" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="True" label="Label rarefaction curves by rownames of X"/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
74 <param name="include_outputs" type="select" multiple="True" label="Datasets to create">
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
75 <option value="output_species_count" selected="true">Count of species</option>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
76 <option value="output_species_frequency" selected="true">Species frequency</option>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
77 <option value="output_richness" selected="true">Richness</option>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
78 <option value="output_species_probabilities" selected="true">Species probabilities</option>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
79 <option value="output_slope" selected="true">Slope of rarefaction curve</option>
1
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
80 <option value="output_plot" selected="true">Rarefaction plot</option>
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
81 <option value="output_random_rarefied" selected="true">Randomly rarefied community matrix</option>
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
82 <option value="output_r_script" selected="false">R script</option>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
83 </param>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
84 </inputs>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
85 <outputs>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
86 <data format="tabular" name="output_species_count" label="${tool.name} on ${on_string} (number of species)">
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
87 <filter>"output_species_count" in include_outputs</filter>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
88 </data>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
89 <data format="tabular" name="output_species_frequency" label="${tool.name} on ${on_string} (frequency of species)">
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
90 <filter>"output_species_frequency" in include_outputs</filter>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
91 </data>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
92 <data format="tabular" name="output_richness" label="${tool.name} on ${on_string} (estimated richness)">
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
93 <filter>"output_richness" in include_outputs</filter>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
94 </data>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
95 <data format="tabular" name="output_species_probabilities" label="${tool.name} on ${on_string} (species probabilities)">
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
96 <filter>"output_species_probabilities" in include_outputs</filter>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
97 </data>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
98 <data format="tabular" name="output_slope" label="${tool.name} on ${on_string} (slope of curve)">
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
99 <filter>"output_slope" in include_outputs</filter>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
100 </data>
1
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
101 <data format="png" name="output_plot" label="${tool.name} on ${on_string} (plot)">
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
102 <filter>"output_plot" in include_outputs</filter>
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
103 </data>
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
104 <data format="tabular" name="output_random_rarefied" label="${tool.name} on ${on_string} (Random rarefied community matrix)">
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
105 <filter>"output_random_rarefied" in include_outputs</filter>
dd2705a31239 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 55b5863db6c3e6cf443917117ec362a8daad8122
iuc
parents: 0
diff changeset
106 </data>
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
107 <data format="txt" name="output_r_script" label="${tool.name} on ${on_string} (Rscript)">
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
108 <filter>"output_r_script" in include_outputs</filter>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
109 </data>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
110 </outputs>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
111 <tests>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
112 <test>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
113 <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
114 <param name="species_column" value="6"/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
115 <param name="sample_columns" value="2"/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
116 <param name="sample_size" value=""/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
117 <param name="step_size" value="1"/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
118 <param name="xlab" value="Sample Size"/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
119 <param name="ylab" value="Species"/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
120 <param name="label" value="TRUE"/>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
121 <output name="output_species_count" ftype="tabular" file="vegan_output_species_count.tabular" />
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
122 <output name="output_species_frequency" ftype="tabular" file="vegan_output_species_frequency.tabular" />
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
123 <output name="output_richness" ftype="tabular" file="vegan_output_richness.tabular" />
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
124 <output name="output_species_probabilities" ftype="tabular" file="vegan_output_species_probabilities.tabular" />
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
125 <output name="output_slope" ftype="tabular" file="vegan_output_slope.tabular" />
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
126 </test>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
127 </tests>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
128 <help>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
129 <![CDATA[
2
b0d5976540e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 1
diff changeset
130
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
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).
2
b0d5976540e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 1
diff changeset
132
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
133 Returns probabilities that species occur in a rarefied community of size sample.
2
b0d5976540e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 1
diff changeset
134
0
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
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.
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
136
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
137
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
138 .. class:: warningmark
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
139
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
140 When subsampling by community size, slope of the rarefaction curve and species probabilities are computed using community size-1
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
141 ]]>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
142 </help>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
143 <citations>
3d1d965b6423 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_rarefaction commit 0e04a4c237677c1f5be1950babcf8591097996a9
iuc
parents:
diff changeset
144 </citations>
2
b0d5976540e3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
iuc
parents: 1
diff changeset
145 </tool>