Mercurial > repos > iuc > qiime_beta_diversity_through_plots

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
author iuc
date Thu, 05 Dec 2019 07:52:18 -0500
parents 2140c12755d0
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70c4237c3a00 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c845cb240f57663cf1e2240c5c506ea0b294872c"
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1 <tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices and generate PCoA plots" version="@WRAPPER_VERSION@.0" profile="@PROFILE@">
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2 <description>(beta_diversity_through_plots)</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <stdio>
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8 <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/>
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9 </stdio>
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10 <version_command>beta_diversity_through_plots.py --version</version_command>
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11 <command detect_errors="aggressive"><![CDATA[
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12 @MPLBACKEND@
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13 beta_diversity_through_plots.py
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14 --otu_table_fp '$otu_table_fp'
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15 --mapping_fp '$mapping_fp'
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16 --output_dir beta_diversity_through_plots
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17 #if $tree_fp
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18 --tree_fp '$tree_fp'
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19 #end if
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20 #if $parameter_fp
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21 --parameter_fp '$parameter_fp'
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22 #end if
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23 $color_by_all_fields
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24 $parallel
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25 -O "\${GALAXY_SLOTS:-4}"
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26 #if $seqs_per_sample
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27 --seqs_per_sample '$seqs_per_sample'
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28 #end if
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29 $suppress_emperor_plots
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30
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31 && python $__tool_directory__/beta_diversity_through_plots_html_generation.py
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32 --data_directory beta_diversity_through_plots
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33 --html_file '$beta_diversity_pcoa'
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34 --html_dir '$beta_diversity_pcoa.files_path'
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35 ]]></command>
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36 <inputs>
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37 <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" multiple="true" label="OTU table"/>
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38 <param argument="--mapping_fp" type="data" format="tabular,txt" multiple="true" label="Mapping file"/>
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39 <param argument="--tree_fp" type="data" format="txt" optional="true" label="Tree file (Optional)"/>
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40 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file (Optional)" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/>
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41 <param argument="--color_by_all_fields" type="text" optional="true" label="Colored mapping fields" help="Can be included only fields with greater than one value and fewer values than the number of samples"/>
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42 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="false" label="Run in parallel where available?"/>
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43 <param argument="--seqs_per_sample" type="integer" optional="true" label="Depth of coverage for even sampling (Optional)"/>
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44 <param argument="--suppress_emperor_plots" type="boolean" truevalue="" falsevalue="--suppress_emperor_plots" checked="true" label="Generate emperor plots?" help=""/>
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45 </inputs>
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46 <outputs>
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47 <collection name="beta_diversity_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for each metrics">
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48 <discover_datasets pattern="(?P&lt;designation&gt;.+)_dm\.txt" ext="txt" directory="beta_diversity_through_plots"/>
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49 </collection>
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50 <collection name="beta_diversity_pc" type="list" label="${tool.name} on ${on_string}: Principal coordinates for each metrics">
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51 <discover_datasets pattern="(?P&lt;designation&gt;.+)_pc\.txt" ext="txt" directory="beta_diversity_through_plots"/>
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52 </collection>
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53 <data format="html" name="beta_diversity_pcoa" label="${tool.name} on ${on_string}: Emperor PCoA plots"/>
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54 </outputs>
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55 <tests>
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56 <test>
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57 <param name="otu_table_fp" value="beta_diversity_through_plots/otu_table.biom"/>
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58 <param name="mapping_fp" value="beta_diversity_through_plots/map.txt"/>
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59 <param name="tree_fp" value="beta_diversity_through_plots/rep_set.tre"/>
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60 <param name="parallel" value="--parallel"/>
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61 <param name="suppress_emperor_plots" value=""/>
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62 <output_collection name="beta_diversity_matrix" type="list" count="2">
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63 <element name="unweighted_unifrac" file="beta_diversity_through_plots/unweighted_unifrac_dm.txt" ftype="txt"/>
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64 <element name="weighted_unifrac" file="beta_diversity_through_plots/weighted_unifrac_dm.txt" ftype="txt"/>
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65 </output_collection>
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66 <output_collection name="beta_diversity_pc" type="list" count="2">
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67 <element name="unweighted_unifrac" ftype="txt">
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68 <assert_contents>
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69 <has_text text="PC.355"/>
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70 <has_text text="Species"/>
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71 <has_text text="Site"/>
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72 </assert_contents>
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73 </element>
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74 <element name="weighted_unifrac" file="beta_diversity_through_plots/weighted_unifrac_pc.txt" ftype="txt"/>
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75 </output_collection>
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76 <output name="beta_diversity_pcoa">
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77 <assert_contents>
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78 <has_text text="unweighted_unifrac" />
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79 <has_text text="weighted_unifrac" />
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80 </assert_contents>
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81 </output>
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82 </test>
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83 </tests>
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84 <help><![CDATA[
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85 **What it does**
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86
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87 This tool computes beta diversity distance matrices and generates PCoA plots in
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88 several steps
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89
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90 - Performs beta diversity analysis
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91 - Performs principal coordinate analysis
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92 - Generates 3D PCoA Plots
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93
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94 More information about this tool is available on
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95 `QIIME documentation <http://qiime.org/scripts/beta_diversity_through_plots.html>`_.
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96 ]]></help>
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97 <citations>
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98 <expand macro="citations"/>
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99 </citations>
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100 </tool>