| Previous changeset 2:b0d5976540e3 (2018-09-07) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit f93edebf6c946402f105f0622aacb0baa216a70c |
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modified:
macros.xml vegan_rarefaction.xml |
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added:
test-data/vegan_output_plot.png test-data/vegan_output_random_rarefied.tabular |
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| diff -r b0d5976540e3 -r af1211ed6c8e macros.xml --- a/macros.xml Fri Sep 07 11:31:02 2018 -0400 +++ b/macros.xml Fri Mar 15 15:26:48 2024 +0000 |
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| @@ -36,6 +36,26 @@ ]]> </token> + + <xml name="bio.tools_xrefs"> + <xrefs> + <xref type="bio.tools">vegan</xref> + </xrefs> + </xml> + + <xml name="citations"> + <citations> + <citation type="bibtex"> + @Manual{, + title = {vegan: Community Ecology Package}, + author = {Jari Oksanen and Gavin L. Simpson and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R.B. O'Hara and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner and Matt Barbour and Michael Bedward and Ben Bolker and Daniel Borcard and Gustavo Carvalho and Michael Chirico and Miquel {De Caceres} and Sebastien Durand and Heloisa Beatriz Antoniazi Evangelista and Rich FitzJohn and Michael Friendly and Brendan Furneaux and Geoffrey Hannigan and Mark O. Hill and Leo Lahti and Dan McGlinn and Marie-Helene Ouellette and Eduardo {Ribeiro Cunha} and Tyler Smith and Adrian Stier and Cajo J.F. {Ter Braak} and James Weedon}, + year = {2024}, + note = {R package version 2.6-5}, + url = {https://github.com/vegandevs/vegan}, + } + </citation> + </citations> + </xml> <token name="@RSCRIPT_PREAMBLE@"><![CDATA[ options(bitmapType='cairo')## No X11, so we'll use cairo |
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| diff -r b0d5976540e3 -r af1211ed6c8e test-data/vegan_output_plot.png |
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| Binary file test-data/vegan_output_plot.png has changed |
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| diff -r b0d5976540e3 -r af1211ed6c8e test-data/vegan_output_random_rarefied.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/vegan_output_random_rarefied.tabular Fri Mar 15 15:26:48 2024 +0000 |
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| @@ -0,0 +1,23 @@ + V2 + Bacteroidetes 4226 + Chlorobi 10 + Firmicutes 1163 + Proteobacteria 402 + Actinobacteria 275 + Cyanobacteria 30 + Acidobacteria 15 + Fibrobacteres 8 + Chloroflexi 12 + Gemmatimonadetes 8 + Aquificae 8 + Tenericutes 7 + Planctomycetes 6 + Nitrospirae 5 + Verrucomicrobia 5 + Thermotogae 5 + Fusobacteria 2 + Deinococcus-Thermus 1 + Elusimicrobia 1 + Deferribacteres 1 + Spirochaetes 1 + Euryarchaeota 1 |
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| diff -r b0d5976540e3 -r af1211ed6c8e vegan_rarefaction.xml --- a/vegan_rarefaction.xml Fri Sep 07 11:31:02 2018 -0400 +++ b/vegan_rarefaction.xml Fri Mar 15 15:26:48 2024 +0000 |
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| @@ -5,6 +5,7 @@ <macros> <import>macros.xml</import> </macros> + <expand macro="bio.tools_xrefs" /> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> @@ -109,7 +110,7 @@ </data> </outputs> <tests> - <test> + <test expect_num_outputs="7"> <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/> <param name="species_column" value="6"/> <param name="sample_columns" value="2"/> @@ -123,6 +124,8 @@ <output name="output_richness" ftype="tabular" file="vegan_output_richness.tabular" /> <output name="output_species_probabilities" ftype="tabular" file="vegan_output_species_probabilities.tabular" /> <output name="output_slope" ftype="tabular" file="vegan_output_slope.tabular" /> + <output name="output_plot" ftype="png" file="vegan_output_plot.png" compare="sim_size" /> + <output name="output_random_rarefied" ftype="tabular" file="vegan_output_random_rarefied.tabular" /> </test> </tests> <help> @@ -140,6 +143,5 @@ When subsampling by community size, slope of the rarefaction curve and species probabilities are computed using community size-1 ]]> </help> - <citations> - </citations> + <expand macro="citations" /> </tool> |
