Mercurial > repos > iuc > ampvis2_alpha_diversity
diff alpha_diversity.xml @ 0:b54f72135f58 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ampvis2 commit 7c0ecbffdb5e993f5af7e3b52c424c2761fb91d3"
| author | iuc |
|---|---|
| date | Mon, 04 Apr 2022 10:26:31 +0000 |
| parents | |
| children | 21b85417e4c3 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/alpha_diversity.xml Mon Apr 04 10:26:31 2022 +0000 @@ -0,0 +1,101 @@ +<tool id="ampvis2_alpha_diversity" name="ampvis2 alpha diversity" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@" license="MIT"> + <description></description> + <macros> + <import>macros.xml</import> + </macros> + <expand macro="header"/> + <command detect_errors="exit_code"><![CDATA[ + Rscript '$rscript' + ]]></command> + <configfiles> + <configfile name="rscript"><![CDATA[ + #set m='"' + '", "'.join(str($measure).split(",")) + '"' + library(ampvis2, quietly = TRUE) + d <- readRDS("$data") + a <- amp_alphadiv(d, + measure = c($m), + richness = $richness + @RAREFY_TOKEN@ + ) + write.table(a, file='$alphadiv', quote=FALSE, sep='\t', row.names=FALSE) + ]]></configfile> + </configfiles> + <inputs> + <expand macro="rds_input_macro"/> + <param argument="measure" type="select" multiple="true" optional="false" label="Alpha-diversity measure(s) to be included"> + <option value="observed" selected="true">observed</option> + <option value="shannon" selected="true">shannon</option> + <option value="simpson" selected="true">simpson</option> + <option value="invsimpson" selected="true">invsimpson</option> + </param> + <param argument="richness" type="boolean" truevalue="TRUE" falsevalue="FALSE" label="Calculate sample richness estimates" help="Chao1 and ACE"/> + <expand macro="rarefy_macro" help="before calculating alpha diversity and/or richnes"/> + </inputs> + <outputs> + <data name="alphadiv" format="tabular"/> + </outputs> + <tests> + <test> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <output name="alphadiv"> + <assert_contents> + <has_line line="SampleID	Plant	Date	Year	Period	Reads	ObservedOTUs	Shannon	Simpson	invSimpson"/> + <has_text text="16SAMP-536	"/> + <has_text text="	Aalborg West	"/> + <has_n_lines n="68"/> + <has_n_columns n="10"/> + </assert_contents> + </output> + </test> + <test> + <param name="data" value="AalborgWWTPs.rds" ftype="ampvis2"/> + <param name="measure" value="observed,shannon"/> + <param name="richness" value="true"/> + <param name="rarefy" value="500"/> + <output name="alphadiv"> + <assert_contents> + <has_line line="SampleID	Plant	Date	Year	Period	RawReads	Reads	ObservedOTUs	Shannon	Chao1	ACE"/> + <has_text text="16SAMP-536	"/> + <has_text text="	Aalborg West	"/> + <has_n_lines n="68"/> + <has_n_columns n="11"/> + <has_text text="	500	"/> + </assert_contents> + </output> + </test> + </tests> + <help><![CDATA[ + +What it does +============ + +Calculate alpha-diversity indices for each sample and combines with the metadata. + +The Galaxy tool calls the `amp_alpha_diversity +<https://madsalbertsen.github.io/ampvis2/reference/amp_alphadiv.html>`_ function +of the ampvis2 package. + +Usage +===== + +The alpha-diversity indices are calculated per sample using the vegan function `diversity <https://rdrr.io/pkg/vegan/man/diversity.html>`_, +where the read abundances are first rarefied using `rrarefy <https://rdrr.io/pkg/vegan/man/rarefy.html>`_ by the size of the rarefy argument. +Refer to the vegan documentation for details about the different indices and how they are +calculated. + + +Input +===== + +@HELP_RDS_INPUT@ + +Output +====== + +A tabular dataset containing the chosen alpha-diversity measures per sample. + + ]]></help> + <expand macro="citations"> + <citation type="doi">10.1371/journal.pcbi.1003531</citation> + </expand> +</tool> \ No newline at end of file