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author devteam
date Wed, 26 Aug 2015 17:11:15 -0400
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8620a6ba883a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/vegan_diversity commit 37144be811dd587897dd9dcb652de0854f049b9a
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1 <tool id="vegan_diversity" name="Vegan Diversity" version="0.0.1">
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2 <description>
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3 index
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4 </description>
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5 <requirements>
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6 <requirement type="package" version="3.2.1">R</requirement>
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7 <requirement type="package" version="2.3-0">vegan</requirement>
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8 </requirements>
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9 <stdio>
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10 <exit_code range="1:" />
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11 <exit_code range=":-1" />
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12 </stdio>
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13 <command><![CDATA[
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14 Rscript "${vegan_diversity_script}"
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15 ]]>
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16 </command>
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17 <configfiles>
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18 <configfile name="vegan_diversity_script"><![CDATA[
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19 #set $int_species_column = int( str( $species_column ) )
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20 #set $fixed_sample_columns = []
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21 #for $sample_col in map( int, str( $sample_columns ).split( "," ) ):
8620a6ba883a planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/vegan_diversity commit 37144be811dd587897dd9dcb652de0854f049b9a
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22 #assert $sample_col != $int_species_column, "Sample label column and sample count columns must not be the same."
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23 #silent $fixed_sample_columns.append( str( $sample_col if $sample_col < $int_species_column else $sample_col-1 ) )
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24 #end for
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25 library(vegan)
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26 input_abundance <- read.table("${input_abundance}", sep="\t", row.names=${ species_column }, header=${header} )
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27 input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )
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28
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29 write.table( diversity(input_abundance, index = "${index_type.index_type_selector}", MARGIN = ${index_type.margin}, base = ${index_type.base}), "${output_diversity_index}", col.names=NA, sep = "\t")
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30 ]]>
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31 </configfile>
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32 </configfiles>
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33 <inputs>
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34 <param name="input_abundance" type="data" format="tabular" label="File with abundance values for community" help="Rows are samples; columns are species/phyla/community classifier"/>
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35 <param name="species_column" label="Group name column" type="data_column" data_ref="input_abundance" value="6" help="Species, phylum, etc"/>
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36 <param name="sample_columns" label="Sample count columns" type="data_column" multiple="True" value="2" data_ref="input_abundance" help="Select each column that contains counts"/>
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37 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Input has a header line"/>
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38 <conditional name="index_type">
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39 <param name="index_type_selector" type="select" label="Diversity index to use">
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40 <option value="shannon" selected="True">shannon</option>
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41 <option value="simpson">simpson</option>
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42 <option value="invsimpson">invsimpson</option>
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43 </param>
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44 <when value="shannon">
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45 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
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46 <param name="base" type="select" label="The logarithm base used in shannon">
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47 <option value="exp(1)" selected="True">exp(1)</option>
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48 <option value="2" selected="False">2</option>
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49 </param>
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50 </when>
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51 <when value="simpson">
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52 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
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53 <param name="base" type="select" label="The logarithm base used in shannon">
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54 <option value="exp(1)" selected="True">exp(1)</option>
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55 <option value="2" selected="False">2</option>
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56 </param>
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57 </when>
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58 <when value="invsimpson">
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59 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
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60 <param name="base" type="select" label="The logarithm base used in shannon">
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61 <option value="exp(1)" selected="True">exp(1)</option>
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62 <option value="2" selected="False">2</option>
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63 </param>
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64 </when>
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65 </conditional>
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66 </inputs>
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67 <outputs>
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68 <data format="tabular" name="output_diversity_index" />
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69 </outputs>
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70 <tests>
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71 <test>
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72 <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
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73 <param name="species_column" value="6"/>
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74 <param name="sample_columns" value="2"/>
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75 <param name="index_type_selector" value="shannon"/>
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76 <param name="margin" value="1"/>
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77 <param name="base" value="exp(1)"/>
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78 <output name="output_slope" ftype="tabular" file="output_diversity_index.tabular" />
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79 </test>
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80 </tests>
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81 <help>
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82 <![CDATA[
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83 Calculate Diversity index using vegan and selected method.
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84 ]]>
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85 </help>
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86 <citations>
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87 </citations>
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88 </tool>