Mercurial > repos > iuc > vegan_diversity

annotate vegan_diversity.xml @ 2:db56c8e79b1e draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_diversity commit bfa8bda732de882f6fa5f5375f8468ad229cceea
author iuc
date Mon, 07 Nov 2016 17:43:22 -0500
parents 2c771b437502
children a2c047a2c380
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1 <tool id="vegan_diversity" name="Vegan Diversity" version="0.0.3">
0
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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>
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12 <![CDATA[
0
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13 Rscript "${vegan_diversity_script}"
c58e19ff504a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_diversity commit 0e04a4c237677c1f5be1950babcf8591097996a9
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14 ]]>
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15 </command>
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16 <configfiles>
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17 <configfile name="vegan_diversity_script"><![CDATA[
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18 @RSCRIPT_PREAMBLE@
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19 @RSCRIPT_LOAD_TABULAR_FILE@
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20
1
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21 write.table( diversity(input_abundance, index = "${index_type.index_type_selector}", MARGIN = ${index_type.margin}, base = ${index_type.base}), "${output_diversity_index}", quote=FALSE, col.names=NA, sep = "\t")
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c58e19ff504a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_diversity commit 0e04a4c237677c1f5be1950babcf8591097996a9
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22 ]]>
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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" />
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27 <conditional name="index_type">
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28 <param name="index_type_selector" type="select" label="Diversity index to use">
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29 <option value="shannon" selected="True">Shannon or Shannon–Weaver (or Shannon–Wiener)</option>
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30 <option value="simpson">Simpson</option>
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31 <option value="invsimpson">Inverse Simpson</option>
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32 </param>
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33 <when value="shannon">
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34 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
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35 <param name="base" type="select" label="The logarithm base">
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36 <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
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37 <option value="2" selected="False">2</option>
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38 </param>
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39 </when>
c58e19ff504a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_diversity commit 0e04a4c237677c1f5be1950babcf8591097996a9
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40 <when value="simpson">
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41 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
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42 <param name="base" type="select" label="The logarithm base">
c58e19ff504a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vegan/vegan_diversity commit 0e04a4c237677c1f5be1950babcf8591097996a9
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43 <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
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44 <option value="2" selected="False">2</option>
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45 </param>
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46 </when>
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47 <when value="invsimpson">
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48 <param name="margin" type="integer" value="1" label="Margin for which the index is computed"/>
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49 <param name="base" type="select" label="The logarithm base">
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50 <option value="exp(1)" selected="True">Natural Logarithm: exp(1)</option>
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51 <option value="2" selected="False">2</option>
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52 </param>
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53 </when>
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54 </conditional>
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55 </inputs>
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56 <outputs>
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57 <data format="tabular" name="output_diversity_index" />
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58 </outputs>
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59 <tests>
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60 <test>
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61 <param name="input_abundance" ftype="tabular" value="vegan_in.tabular"/>
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62 <param name="species_column" value="6"/>
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63 <param name="sample_columns" value="2"/>
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64 <param name="index_type_selector" value="shannon"/>
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65 <param name="margin" value="1"/>
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66 <param name="base" value="exp(1)"/>
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67 <output name="output_slope" ftype="tabular" file="output_diversity_index.tabular" />
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68 </test>
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69 </tests>
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70 <help>
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71 <![CDATA[
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72 Calculate Diversity index using vegan and selected method.
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73 ]]>
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74 </help>
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75 <citations>
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76 </citations>
2
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77 </tool>