Mercurial > repos > iuc > vegan_diversity
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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_diversity commit bfa8bda732de882f6fa5f5375f8468ad229cceea
author | iuc |
---|---|
date | Mon, 07 Nov 2016 17:43:22 -0500 |
parents | 2c771b437502 |
children | a2c047a2c380 |
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<tool id="vegan_diversity" name="Vegan Diversity" version="0.0.3"> <description> index </description> <macros> <import>vegan_macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <expand macro="version_command" /> <command> <![CDATA[ Rscript "${vegan_diversity_script}" ]]> </command> <configfiles> <configfile name="vegan_diversity_script"><![CDATA[ @RSCRIPT_PREAMBLE@ @RSCRIPT_LOAD_TABULAR_FILE@ write.table( diversity(input_abundance, index = "${index_type.index_type_selector}", MARGIN = ${index_type.margin}, base = ${index_type.base}), "${output_diversity_index}", quote=FALSE, col.names=NA, sep = "\t") ]]> </configfile> </configfiles> <inputs> <expand macro="params_load_tabular_file" /> <conditional name="index_type"> <param name="index_type_selector" type="select" label="Diversity index to use"> <option value="shannon" selected="True">Shannon or Shannon–Weaver (or Shannon–Wiener)</option> <option value="simpson">Simpson</option> <option value="invsimpson">Inverse Simpson</option> </param> <when value="shannon"> <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/> <param name="base" type="select" label="The logarithm base"> <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option> <option value="2" selected="False">2</option> </param> </when> <when value="simpson"> <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/> <param name="base" type="select" label="The logarithm base"> <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option> <option value="2" selected="False">2</option> </param> </when> <when value="invsimpson"> <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/> <param name="base" type="select" label="The logarithm base"> <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option> <option value="2" selected="False">2</option> </param> </when> </conditional> </inputs> <outputs> <data format="tabular" name="output_diversity_index" /> </outputs> <tests> <test> <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/> <param name="species_column" value="6"/> <param name="sample_columns" value="2"/> <param name="index_type_selector" value="shannon"/> <param name="margin" value="1"/> <param name="base" value="exp(1)"/> <output name="output_slope" ftype="tabular" file="output_diversity_index.tabular" /> </test> </tests> <help> <![CDATA[ Calculate Diversity index using vegan and selected method. ]]> </help> <citations> </citations> </tool>