Mercurial > repos > iuc > picrust_predict_metagenomes

annotate predict_metagenomes.xml @ 0:2d4c0825cfe6 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
author iuc
date Thu, 08 Dec 2016 06:28:50 -0500
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2d4c0825cfe6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picrust commit a933cd08ace9778a03e575e54f2b69bc5315e14c
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1 <tool id="picrust_predict_metagenomes" name="Predict Metagenome" version="@WRAPPER_VERSION@.0">
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2 <description>create a virtual metagenome of KEGG Ortholog abundances</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 <expand macro="version_command"/>
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8 <command detect_errors="aggressive"><![CDATA[
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9 predict_metagenomes.py
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10 -i '$input_data'
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11 -o tempbiom
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12 -c '$gg.precalc'
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13 $normalize_by_otu
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14 $normalize_by_function
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15 #if $accuracy_metrics:
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16 -a $out_summary
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17 #end if
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18
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19 @OUTPUT_CONVERSION_COMMANDS@
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20 ]]></command>
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21 <inputs>
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22 <param name="input_data" type="data" format="tabular,biom1" label="Input file"/>
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23 <expand macro="otu-reference-precalculated"/>
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24 <expand macro="biom_format_select"/>
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25 <param argument="normalize_by_function" type="boolean" truevalue="--normalize_by_function" falsevalue="" checked="false" label="Normalize by function?"
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26 help="Normalizes the predicted functional abundances by dividing each abundance by the sum of functional abundances in the sample. Total sum of abundances for each sample will equal 1"/>
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27 <param argument="normalize_by_otu" type="boolean" truevalue="--normalize_by_otu" falsevalue="" checked="false" label="Normalize by OTU?"
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28 help="Normalizes the predicted functional abundances by dividing each abundance by the sum of OTUs in the sample. Note: total sum of abundances for each sample will NOT equal 1"/>
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29 <param argument="accuracy_metrics" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Calculate accuracy metrics"
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30 help="requires that per-genome accuracy metrics were calculated during genome prediction (predict_traits tool) (e.g. there are NSTI values in the genome biom file metadata)"/>
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31 </inputs>
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32 <outputs>
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33 <expand macro="biom_output"/>
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34 <data name="out_summary" format="tabular">
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35 <filter>accuracy_metrics</filter>
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36 </data>
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37 </outputs>
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38 <tests>
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39 <test> <!-- test with defaults -->
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40 <param name="input_data" value="normalized_otus.biom"/>
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41 <param name="source" value="hist"/>
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42 <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
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43 <param name="output_type" value="json"/>
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44 <output name="out_file" ftype="json">
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45 <assert_contents>
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46 <has_text text="Biological Observation Matrix"/>
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47 <has_text text="generated_by"/>
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48 </assert_contents>
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49 </output>
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50 </test>
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51 <test> <!-- test with accuracy metrics and normalizations -->
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52 <param name="input_data" value="otu_table_for_custom_trait_table.biom"/>
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53 <param name="source" value="hist"/>
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54 <param name="precalc" value="custom_trait_table.tab"/>
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55 <param name="output_type" value="tsv"/>
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56 <param name="accuracy_metrics" value="T"/>
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57 <param name="normalize_by_function" value="--normalize_by_function"/>
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58 <param name="normalize_by_otu" value="--normalize_by_otu"/>
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59 <output name="out_file" ftype="tabular">
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60 <assert_contents>
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61 <has_text text="trait2"/>
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62 <has_text text="Sample4"/>
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63 </assert_contents>
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64 </output>
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65 <output name="out_summary" ftype="tabular">
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66 <assert_contents>
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67 <has_line_matching expression="#Sample\tMetric\tValue"/>
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68 <has_text text="NSTI"/>
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69 <has_text text="Sample4"/>
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70 </assert_contents>
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71 </output>
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72 </test>
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73 </tests>
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74 <help>
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75 <![CDATA[
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76 @PICRUST_OVERVIEW@
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77
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78 **Command Documentation**
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79
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80 This module produces a 'virtual' metagenome of KEGG Ortholog abundances for each sample in the given OTU table.
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81
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82 **Input file:** This should be a normalized OTU table populated by the output of the PICRUSt Normalize by Copy Number module.
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83
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84 ]]>
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85 </help>
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86 <expand macro="citations"/>
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87 </tool>