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author | bebatut |
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date | Tue, 02 Feb 2016 05:50:37 -0500 |
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<tool id="qiime_alpha_diversity" name="Calculate alpha diversity" version="1.9.1"> <description>on each sample in an otu table</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <version_command><![CDATA[ alpha_diversity.py --version ]]> </version_command> <command> <![CDATA[ #set $chosen_metrics = str( $metrics ).split( "," ) alpha_diversity.py -i $input_table -o $alpha_diversity -m $metrics #if "PD_whole_tree" in $chosen_metrics: -t $tree_file #end if ]]> </command> <inputs> <param name="input_table" type="data" format="tabular,txt,tsv,biom" label="OTU table" help="(-i/--input_path)" multiple="True"/> <param name="metrics" type="select" multiple="True" label="Alpha-diversity metric(s) to use" help="(-m/--metrics)" display="checkboxes"> <option value="ace">ACE (Abundance-based Coverage Estimator) metric</option> <option value="berger_parker_d">Berger-Parker dominance</option> <option value="brillouin_d">Brillouin index of alpha diversity</option> <option value="chao1" selected="true">chao1 richness estimator</option> <option value="chao1_ci">chao1 confidence interval</option> <option value="dominance">Dominance</option> <option value="doubles">Number of double occurrences (doubletons)</option> <option value="enspie">ENS_pie alpha diversity measure</option> <option value="equitability">Equitability</option> <option value="esty_ci">Esty’s CI</option> <option value="fisher_alpha">Fisher’s alpha</option> <option value="gini_index">Gini index</option> <option value="goods_coverage">Good’s coverage of counts</option> <option value="heip_e">Heip’s evenness measure</option> <option value="kempton_taylor_q">Kempton-Taylor Q index of alpha diversity</option> <option value="margalef">Margalef’s richness index</option> <option value="mcintosh_d">McIntosh dominance index D</option> <option value="mcintosh_e">McIntosh’s evenness measure E</option> <option value="menhinick">Menhinick’s richness index</option> <option value="michaelis_menten_fit">Michaelis-Menten fit to rarefaction curve of observed OTUs</option> <option value="observed_otus">Number of distinct OTUs</option> <option value="observed_species" selected="true">Number of distinct species</option> <option value="osd">Observed OTUs, singles, and doubles</option> <option value="simpson_reciprocal">simpson_reciprocal</option> <option value="robbins">Robbins’ estimator for the probability of unobserved outcomes</option> <option value="shannon">Shannon entropy of counts</option> <option value="simpson">Simpson’s index</option> <option value="simpson_e">Simpson’s evenness measure E</option> <option value="singles">Number of single occurrencesles</option> <option value="strong"> Strong’s dominance index</option> <option value="PD_whole_tree">Phylogenetic diversity</option> </param> <param name="tree_file" type="data" label="Newick tree (optional, except for PD_whole_tree metric" help="(-t/--tree_path)" optional="True"/> </inputs> <outputs> <data name="alpha_diversity" format="tabular" from_work_dir="alpha_diversity/alpha_div.txt" label="${tool.name} on ${on_string}: Alpha diversity" /> </outputs> <tests> <test> <param name="input_table" value="pick_open_reference_otus_otu_table.txt"/> <param name="metrics" value="chao1,observed_species" /> <output name="alpha_diversity" value="" /> </test> </tests> <help><![CDATA[ **What it does?** This tool calculates alpha diversity, or within-sample diversity, using an OTU table. The resulting file(s) is a tab-delimited text file, where the columns correspond to alpha diversity metrics and the rows correspond to samples and their calculated diversity measurements. When a folder is given as input (-i), the script processes every otu table file in the given folder, and creates a corresponding file in the output directory. More information about this tool is available on `QIIME documentation <http://qiime.org/scripts/alpha_diversity.html>`_. ]]> </help> <citations> <expand macro="citations" /> </citations> </tool>