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comparison vegan_diversity.xml @ 0:8620a6ba883a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/vegan_diversity commit 37144be811dd587897dd9dcb652de0854f049b9a
author devteam
date Wed, 26 Aug 2015 17:11:15 -0400
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-1:000000000000 0:8620a6ba883a
1 <tool id="vegan_diversity" name="Vegan Diversity" version="0.0.1">
2 <description>
3 index
4 </description>
5 <requirements>
6 <requirement type="package" version="3.2.1">R</requirement>
7 <requirement type="package" version="2.3-0">vegan</requirement>
8 </requirements>
9 <stdio>
10 <exit_code range="1:" />
11 <exit_code range=":-1" />
12 </stdio>
13 <command><![CDATA[
14 Rscript "${vegan_diversity_script}"
15 ]]>
16 </command>
17 <configfiles>
18 <configfile name="vegan_diversity_script"><![CDATA[
19 #set $int_species_column = int( str( $species_column ) )
20 #set $fixed_sample_columns = []
21 #for $sample_col in map( int, str( $sample_columns ).split( "," ) ):
22 #assert $sample_col != $int_species_column, "Sample label column and sample count columns must not be the same."
23 #silent $fixed_sample_columns.append( str( $sample_col if $sample_col < $int_species_column else $sample_col-1 ) )
24 #end for
25 library(vegan)
26 input_abundance <- read.table("${input_abundance}", sep="\t", row.names=${ species_column }, header=${header} )
27 input_abundance <- t( input_abundance[ c( ${ ",".join( $fixed_sample_columns ) } )] )
28
29 write.table( diversity(input_abundance, index = "${index_type.index_type_selector}", MARGIN = ${index_type.margin}, base = ${index_type.base}), "${output_diversity_index}", col.names=NA, sep = "\t")
30 ]]>
31 </configfile>
32 </configfiles>
33 <inputs>
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"/>
35 <param name="species_column" label="Group name column" type="data_column" data_ref="input_abundance" value="6" help="Species, phylum, etc"/>
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"/>
37 <param name="header" type="boolean" truevalue="TRUE" falsevalue="FALSE" checked="False" label="Input has a header line"/>
38 <conditional name="index_type">
39 <param name="index_type_selector" type="select" label="Diversity index to use">
40 <option value="shannon" selected="True">shannon</option>
41 <option value="simpson">simpson</option>
42 <option value="invsimpson">invsimpson</option>
43 </param>
44 <when value="shannon">
45 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
46 <param name="base" type="select" label="The logarithm base used in shannon">
47 <option value="exp(1)" selected="True">exp(1)</option>
48 <option value="2" selected="False">2</option>
49 </param>
50 </when>
51 <when value="simpson">
52 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
53 <param name="base" type="select" label="The logarithm base used in shannon">
54 <option value="exp(1)" selected="True">exp(1)</option>
55 <option value="2" selected="False">2</option>
56 </param>
57 </when>
58 <when value="invsimpson">
59 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
60 <param name="base" type="select" label="The logarithm base used in shannon">
61 <option value="exp(1)" selected="True">exp(1)</option>
62 <option value="2" selected="False">2</option>
63 </param>
64 </when>
65 </conditional>
66 </inputs>
67 <outputs>
68 <data format="tabular" name="output_diversity_index" />
69 </outputs>
70 <tests>
71 <test>
72 <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
73 <param name="species_column" value="6"/>
74 <param name="sample_columns" value="2"/>
75 <param name="index_type_selector" value="shannon"/>
76 <param name="margin" value="1"/>
77 <param name="base" value="exp(1)"/>
78 <output name="output_slope" ftype="tabular" file="output_diversity_index.tabular" />
79 </test>
80 </tests>
81 <help>
82 <![CDATA[
83 Calculate Diversity index using vegan and selected method.
84 ]]>
85 </help>
86 <citations>
87 </citations>
88 </tool>