Mercurial > repos > iuc > vegan_fisher_alpha

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit f93edebf6c946402f105f0622aacb0baa216a70c
author iuc
date Fri, 15 Mar 2024 15:26:28 +0000
parents f9966e11885b
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f9966e11885b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/ commit e0cd7ae10ce97bed51594e7cc0b969a803d698b7
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1 <tool id="vegan_fisher_alpha" name="Vegan Fisher Alpha" version="@TOOL_VERSION@">
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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>macros.xml</import>
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7 </macros>
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8 <expand macro="bio.tools_xrefs" />
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9 <expand macro="requirements" />
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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10 <expand macro="stdio" />
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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11 <expand macro="version_command" />
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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12 <command><![CDATA[
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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13 Rscript "${vegan_fisher_alpha_script}"
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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14 ]]>
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15 </command>
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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16 <configfiles>
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17 <configfile name="vegan_fisher_alpha_script"><![CDATA[
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18 @RSCRIPT_PREAMBLE@
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19 @RSCRIPT_LOAD_TABULAR_FILE@
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20
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21 write.table( fisher.alpha( input_abundance, MARGIN = ${margin} ), "${output_fisher_alpha}", quote=FALSE, col.names=NA, sep = "\t")
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22 ]]>
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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23 </configfile>
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24 </configfiles>
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25 <inputs>
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26 <expand macro="params_load_tabular_file" />
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 <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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28 </inputs>
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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29 <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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30 <data format="tabular" name="output_fisher_alpha" />
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 </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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32 <tests>
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33 <test expect_num_outputs="1">
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34 <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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35 <param name="species_column" value="6"/>
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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36 <param name="sample_columns" value="2"/>
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 <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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38 <output name="output_fisher_alpha" ftype="tabular" file="output_fisher_alpha.tabular" />
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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39 </test>
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40 </tests>
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41 <help>
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42 <![CDATA[
a5a453f92273 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_fisher_alpha commit 0e04a4c237677c1f5be1950babcf8591097996a9
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43 Calculate Diversity index using vegan and selected method.
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44 ]]>
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45 </help>
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46 <expand macro="citations" />
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47 </tool>