Mercurial > repos > iuc > vegan_fisher_alpha

comparison vegan_fisher_alpha.xml @ 0:a5a453f92273 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
author iuc
date Wed, 23 Dec 2015 13:55:34 -0500
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children d6b92ca3a9a1
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-1:000000000000 0:a5a453f92273
1 <tool id="vegan_fisher_alpha" name="Vegan Fisher Alpha" 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_fisher_alpha_script}"
13 ]]>
14 </command>
15 <configfiles>
16 <configfile name="vegan_fisher_alpha_script"><![CDATA[
17 @RSCRIPT_PREAMBLE@
18 @RSCRIPT_LOAD_TABULAR_FILE@
19
20 write.table( fisher.alpha( input_abundance, MARGIN = ${margin} ), "${output_fisher_alpha}", col.names=NA, sep = "\t")
21 ]]>
22 </configfile>
23 </configfiles>
24 <inputs>
25 <expand macro="params_load_tabular_file" />
26 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
27 </inputs>
28 <outputs>
29 <data format="tabular" name="output_fisher_alpha" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
34 <param name="species_column" value="6"/>
35 <param name="sample_columns" value="2"/>
36 <param name="margin" value="1"/>
37 <output name="output_fisher_alpha" ftype="tabular" file="output_fisher_alpha.tabular" />
38 </test>
39 </tests>
40 <help>
41 <![CDATA[
42 Calculate Diversity index using vegan and selected method.
43 ]]>
44 </help>
45 <citations>
46 </citations>
47 </tool>