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comparison vegan_diversity.xml @ 0:c58e19ff504a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_diversity commit 0e04a4c237677c1f5be1950babcf8591097996a9
author iuc
date Wed, 23 Dec 2015 13:55:10 -0500
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children 2c771b437502
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-1:000000000000 0:c58e19ff504a
1 <tool id="vegan_diversity" name="Vegan Diversity" version="0.0.2">
2 <description>
3 index
4 </description>
5 <macros>
6 <import>vegan_macros.xml</import>
7 </macros>
8 <expand macro="requirements" />
9 <expand macro="stdio" />
10 <expand macro="version_command" />
11 <command><![CDATA[
12 Rscript "${vegan_diversity_script}"
13 ]]>
14 </command>
15 <configfiles>
16 <configfile name="vegan_diversity_script"><![CDATA[
17 @RSCRIPT_PREAMBLE@
18 @RSCRIPT_LOAD_TABULAR_FILE@
19
20 write.table( diversity(input_abundance, index = "${index_type.index_type_selector}", MARGIN = ${index_type.margin}, base = ${index_type.base}), "${output_diversity_index}", col.names=NA, sep = "\t")
21 ]]>
22 </configfile>
23 </configfiles>
24 <inputs>
25 <expand macro="params_load_tabular_file" />
26 <conditional name="index_type">
27 <param name="index_type_selector" type="select" label="Diversity index to use">
28 <option value="shannon" selected="True">Shannon or Shannon–Weaver (or Shannon–Wiener)</option>
29 <option value="simpson">Simpson</option>
30 <option value="invsimpson">Inverse Simpson</option>
31 </param>
32 <when value="shannon">
33 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
34 <param name="base" type="select" label="The logarithm base">
35 <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
36 <option value="2" selected="False">2</option>
37 </param>
38 </when>
39 <when value="simpson">
40 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
41 <param name="base" type="select" label="The logarithm base">
42 <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
43 <option value="2" selected="False">2</option>
44 </param>
45 </when>
46 <when value="invsimpson">
47 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
48 <param name="base" type="select" label="The logarithm base">
49 <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
50 <option value="2" selected="False">2</option>
51 </param>
52 </when>
53 </conditional>
54 </inputs>
55 <outputs>
56 <data format="tabular" name="output_diversity_index" />
57 </outputs>
58 <tests>
59 <test>
60 <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
61 <param name="species_column" value="6"/>
62 <param name="sample_columns" value="2"/>
63 <param name="index_type_selector" value="shannon"/>
64 <param name="margin" value="1"/>
65 <param name="base" value="exp(1)"/>
66 <output name="output_slope" ftype="tabular" file="output_diversity_index.tabular" />
67 </test>
68 </tests>
69 <help>
70 <![CDATA[
71 Calculate Diversity index using vegan and selected method.
72 ]]>
73 </help>
74 <citations>
75 </citations>
76 </tool>