Mercurial > repos > iuc > vegan_fisher_alpha

annotate vegan_fisher_alpha.xml @ 1:d6b92ca3a9a1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 55b5863db6c3e6cf443917117ec362a8daad8122
author iuc
date Mon, 08 Feb 2016 15:24:35 -0500
parents a5a453f92273
children f9966e11885b
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d6b92ca3a9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 55b5863db6c3e6cf443917117ec362a8daad8122
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1 <tool id="vegan_fisher_alpha" name="Vegan Fisher Alpha" version="0.0.3">
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2 <description>
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3 index
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4 </description>
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5 <macros>
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6 <import>vegan_macros.xml</import>
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7 </macros>
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8 <expand macro="requirements" />
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9 <expand macro="stdio" />
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10 <expand macro="version_command" />
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11 <command><![CDATA[
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12 Rscript "${vegan_fisher_alpha_script}"
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13 ]]>
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14 </command>
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15 <configfiles>
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16 <configfile name="vegan_fisher_alpha_script"><![CDATA[
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17 @RSCRIPT_PREAMBLE@
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18 @RSCRIPT_LOAD_TABULAR_FILE@
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19
1
d6b92ca3a9a1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 55b5863db6c3e6cf443917117ec362a8daad8122
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20 write.table( fisher.alpha( input_abundance, MARGIN = ${margin} ), "${output_fisher_alpha}", quote=FALSE, col.names=NA, sep = "\t")
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21 ]]>
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22 </configfile>
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23 </configfiles>
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24 <inputs>
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25 <expand macro="params_load_tabular_file" />
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26 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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27 </inputs>
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28 <outputs>
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29 <data format="tabular" name="output_fisher_alpha" />
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30 </outputs>
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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31 <tests>
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32 <test>
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33 <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
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34 <param name="species_column" value="6"/>
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35 <param name="sample_columns" value="2"/>
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36 <param name="margin" value="1"/>
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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37 <output name="output_fisher_alpha" ftype="tabular" file="output_fisher_alpha.tabular" />
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38 </test>
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39 </tests>
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40 <help>
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41 <![CDATA[
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42 Calculate Diversity index using vegan and selected method.
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43 ]]>
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44 </help>
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45 <citations>
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46 </citations>
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47 </tool>