Mercurial > repos > iuc > qiime_beta_diversity_through_plots
comparison beta_diversity_through_plots.xml @ 0:e5b102db53fd draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit c9bf747b23b4a9d6adc20c7740b9247c22654862
| author | iuc |
|---|---|
| date | Thu, 18 May 2017 09:34:39 -0400 |
| parents | |
| children | 2140c12755d0 |
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| -1:000000000000 | 0:e5b102db53fd |
|---|---|
| 1 <tool id="qiime_beta_diversity_through_plots" name="Compute beta diversity distance matrices" version="@WRAPPER_VERSION@.0"> | |
| 2 <description>and generate PCoA plots</description> | |
| 3 <macros> | |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements"/> | |
| 7 <stdio> | |
| 8 <regex match="VisibleDeprecationWarning" source="both" level="warning" description="VisibleDeprecationWarning on numpy for `rank`"/> | |
| 9 </stdio> | |
| 10 <version_command>beta_diversity_through_plots.py --version</version_command> | |
| 11 <command detect_errors="aggressive"><![CDATA[ | |
| 12 beta_diversity_through_plots.py | |
| 13 --otu_table_fp '$otu_table_fp' | |
| 14 --mapping_fp '$mapping_fp' | |
| 15 --output_dir beta_diversity_through_plots | |
| 16 #if $tree_fp | |
| 17 --tree_fp '$tree_fp' | |
| 18 #end if | |
| 19 #if $parameter_fp | |
| 20 --parameter_fp '$parameter_fp' | |
| 21 #end if | |
| 22 $color_by_all_fields | |
| 23 $parallel | |
| 24 -O "\${GALAXY_SLOTS:-4}" | |
| 25 #if $seqs_per_sample | |
| 26 --seqs_per_sample '$seqs_per_sample' | |
| 27 #end if | |
| 28 $suppress_emperor_plots | |
| 29 | |
| 30 && python $__tool_directory__/beta_diversity_through_plots_html_generation.py | |
| 31 --data_directory beta_diversity_through_plots | |
| 32 --html_file '$beta_diversity_pcoa' | |
| 33 --html_dir '$beta_diversity_pcoa.files_path' | |
| 34 ]]></command> | |
| 35 <inputs> | |
| 36 <param argument="--otu_table_fp" type="data" format="tabular,txt,biom" multiple="True" label="OTU table"/> | |
| 37 <param argument="--mapping_fp" type="data" format="tabular,txt" multiple="True" label="Mapping file" help=""/> | |
| 38 <param argument="--tree_fp" type="data" format="txt" optional="True" label="Tree file (Optional)" help=""/> | |
| 39 <param argument="--parameter_fp" type="data" format="txt" label="Parameter file (Optional)" help="It specifies changes to the default behavior, e.g. beta diversity metrics" optional="true"/> | |
| 40 <param argument="--color_by_all_fields" type="text" optional="True" label="Colored mapping fields" help="Can be included only fields with greater than one value and fewer values than the number of samples"/> | |
| 41 <param argument="--parallel" type="boolean" truevalue="--parallel" falsevalue="" checked="False" label="Run in parallel where available?" help=""/> | |
| 42 <param argument="--seqs_per_sample" type="integer" optional="True" label="Depth of coverage for even sampling (Optional)" help=""/> | |
| 43 <param argument="--suppress_emperor_plots" type="boolean" truevalue="" falsevalue="--suppress_emperor_plots" checked="True" label="Generate emperor plots?" help=""/> | |
| 44 </inputs> | |
| 45 <outputs> | |
| 46 <collection name="beta_diversity_matrix" type="list" label="${tool.name} on ${on_string}: Distance matrix for each metrics"> | |
| 47 <discover_datasets pattern="(?P<designation>.+)_dm\.txt" ext="txt" directory="beta_diversity_through_plots"/> | |
| 48 </collection> | |
| 49 <collection name="beta_diversity_pc" type="list" label="${tool.name} on ${on_string}: Principal coordinates for each metrics"> | |
| 50 <discover_datasets pattern="(?P<designation>.+)_pc\.txt" ext="txt" directory="beta_diversity_through_plots"/> | |
| 51 </collection> | |
| 52 <data format="html" name="beta_diversity_pcoa" label="${tool.name} on ${on_string}: Emperor PCoA plots"/> | |
| 53 </outputs> | |
| 54 <tests> | |
| 55 <test> | |
| 56 <param name="otu_table_fp" value="beta_diversity_through_plots/otu_table.biom"/> | |
| 57 <param name="mapping_fp" value="beta_diversity_through_plots/map.txt"/> | |
| 58 <param name="tree_fp" value="beta_diversity_through_plots/rep_set.tre"/> | |
| 59 <param name="parallel" value="--parallel"/> | |
| 60 <param name="suppress_emperor_plots" value=""/> | |
| 61 <output_collection name="beta_diversity_matrix" type="list" count="2"> | |
| 62 <element name="unweighted_unifrac" file="beta_diversity_through_plots/unweighted_unifrac_dm.txt" ftype="txt"/> | |
| 63 <element name="weighted_unifrac" file="beta_diversity_through_plots/weighted_unifrac_dm.txt" ftype="txt"/> | |
| 64 </output_collection> | |
| 65 <output_collection name="beta_diversity_pc" type="list" count="2"> | |
| 66 <element name="unweighted_unifrac" ftype="txt"> | |
| 67 <assert_contents> | |
| 68 <has_text text="PC.355"/> | |
| 69 <has_text text="Species"/> | |
| 70 <has_text text="Site"/> | |
| 71 </assert_contents> | |
| 72 </element> | |
| 73 <element name="weighted_unifrac" file="beta_diversity_through_plots/weighted_unifrac_pc.txt" ftype="txt"/> | |
| 74 </output_collection> | |
| 75 <output name="beta_diversity_pcoa"> | |
| 76 <assert_contents> | |
| 77 <has_text text="unweighted_unifrac" /> | |
| 78 <has_text text="weighted_unifrac" /> | |
| 79 </assert_contents> | |
| 80 </output> | |
| 81 </test> | |
| 82 </tests> | |
| 83 <help><![CDATA[ | |
| 84 **What it does** | |
| 85 | |
| 86 This tool computes beta diversity distance matrices and generates PCoA plots in | |
| 87 several steps | |
| 88 | |
| 89 - Performs beta diversity analysis | |
| 90 - Performs principal coordinate analysis | |
| 91 - Generates 3D PCoA Plots | |
| 92 | |
| 93 More information about this tool is available on | |
| 94 `QIIME documentation <http://qiime.org/scripts/beta_diversity_through_plots.html>`_. | |
| 95 ]]></help> | |
| 96 <citations> | |
| 97 <expand macro="citations"/> | |
| 98 </citations> | |
| 99 </tool> |