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comparison 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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-1:000000000000 0:2d4c0825cfe6
1 <tool id="picrust_predict_metagenomes" name="Predict Metagenome" version="@WRAPPER_VERSION@.0">
2 <description>create a virtual metagenome of KEGG Ortholog abundances</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version_command"/>
8 <command detect_errors="aggressive"><![CDATA[
9 predict_metagenomes.py
10 -i '$input_data'
11 -o tempbiom
12 -c '$gg.precalc'
13 $normalize_by_otu
14 $normalize_by_function
15 #if $accuracy_metrics:
16 -a $out_summary
17 #end if
18
19 @OUTPUT_CONVERSION_COMMANDS@
20 ]]></command>
21 <inputs>
22 <param name="input_data" type="data" format="tabular,biom1" label="Input file"/>
23 <expand macro="otu-reference-precalculated"/>
24 <expand macro="biom_format_select"/>
25 <param argument="normalize_by_function" type="boolean" truevalue="--normalize_by_function" falsevalue="" checked="false" label="Normalize by function?"
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"/>
27 <param argument="normalize_by_otu" type="boolean" truevalue="--normalize_by_otu" falsevalue="" checked="false" label="Normalize by OTU?"
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"/>
29 <param argument="accuracy_metrics" type="boolean" truevalue="T" falsevalue="F" checked="false" label="Calculate accuracy metrics"
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)"/>
31 </inputs>
32 <outputs>
33 <expand macro="biom_output"/>
34 <data name="out_summary" format="tabular">
35 <filter>accuracy_metrics</filter>
36 </data>
37 </outputs>
38 <tests>
39 <test> <!-- test with defaults -->
40 <param name="input_data" value="normalized_otus.biom"/>
41 <param name="source" value="hist"/>
42 <param name="precalc" value="16S_13_5_precalculated_minimal.tab"/>
43 <param name="output_type" value="json"/>
44 <output name="out_file" ftype="json">
45 <assert_contents>
46 <has_text text="Biological Observation Matrix"/>
47 <has_text text="generated_by"/>
48 </assert_contents>
49 </output>
50 </test>
51 <test> <!-- test with accuracy metrics and normalizations -->
52 <param name="input_data" value="otu_table_for_custom_trait_table.biom"/>
53 <param name="source" value="hist"/>
54 <param name="precalc" value="custom_trait_table.tab"/>
55 <param name="output_type" value="tsv"/>
56 <param name="accuracy_metrics" value="T"/>
57 <param name="normalize_by_function" value="--normalize_by_function"/>
58 <param name="normalize_by_otu" value="--normalize_by_otu"/>
59 <output name="out_file" ftype="tabular">
60 <assert_contents>
61 <has_text text="trait2"/>
62 <has_text text="Sample4"/>
63 </assert_contents>
64 </output>
65 <output name="out_summary" ftype="tabular">
66 <assert_contents>
67 <has_line_matching expression="#Sample\tMetric\tValue"/>
68 <has_text text="NSTI"/>
69 <has_text text="Sample4"/>
70 </assert_contents>
71 </output>
72 </test>
73 </tests>
74 <help>
75 <![CDATA[
76 @PICRUST_OVERVIEW@
77
78 **Command Documentation**
79
80 This module produces a 'virtual' metagenome of KEGG Ortholog abundances for each sample in the given OTU table.
81
82 **Input file:** This should be a normalized OTU table populated by the output of the PICRUSt Normalize by Copy Number module.
83
84 ]]>
85 </help>
86 <expand macro="citations"/>
87 </tool>