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comparison humann_infer_taxonomy @ 0:26ce946f4da9 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann commit 077b8f34e081e6c427acb0fde0fbb97d1b241e0b"
author iuc
date Wed, 12 May 2021 08:59:30 +0000
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-1:000000000000 0:26ce946f4da9
1 <!-- The tool is broken with current version of HUMAnN. Once it will be fixed, we can update this wrapper and add the XML extension to enable it -->
2 <tool id="humann_infer_taxonomy" name="Infex taxonomy" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
3 <description>for "unclassified" taxonomy in HUMAnN generated gene families</description>
4 <macros>
5 <import>macros.xml</import>
6 </macros>
7 <expand macro="edam_ontology"/>
8 <expand macro="requirements"/>
9 <expand macro="version"/>
10 <command detect_errors="exit_code"><![CDATA[
11 humann_infer_taxonomy
12 --input '$input'
13 --output '$output'
14 --level '$level'
15 --database '$database.fields.path'
16 --mode '$mode'
17 --lca-choice '$lca_choice'
18 --threshold $threshold
19 ]]></command>
20 <inputs>
21 <param argument="--input" type="data" format="tsv,tabular" label="Gene family table"/>
22 <param argument="--level" type="select" label="Desired level for taxonomic estimation/summation">
23 <option value="Kingdom">Kingdom</option>
24 <option value="Phylum">Phylum</option>
25 <option value="Class">Class</option>
26 <option value="Order">Order</option>
27 <option value="Family" selected="true">Family</option>
28 <option value="Genus">Genus</option>
29 </param>
30 <param argument="--database" type="select" label="UniRef-specific taxonomy database">
31 <options from_data_table="humann_utility_mapping">
32 <validator message="No utility mapping is available" type="no_options" />
33 <filter type="regexp" column="2" value="tol-lca" />
34 </options>
35 </param>
36 <param argument="--mode" type="select" label="Rows to include in the estimation/summation">
37 <option value="c_tmode" selected="true">Totals</option>
38 <option value="c_umode">Unclassified</option>
39 <option value="c_smode">Stratified</option>
40 </param>
41 <param argument="--lca-choice" type="select" label="Per-gene taxonomic annotation to consider">
42 <option value="source_tax">Source taxonomy</option>
43 <option value="uniref_lca">UniRef lowest common ancestor (LCA)</option>
44 <option value="humann_lca" selected="true">HUMAnN lowest common ancestor (LCA)</option>
45 </param>
46 <param argument="--threshold" type="float" value="1e-3" label="Minimum frequency for a new taxon to be included"/>
47 </inputs>
48 <outputs>
49 <data format="tabular" name="output"/>
50 </outputs>
51 <tests>
52 <test expect_num_outputs="1">
53 <param name="input" value=""/>
54 <param name="level" value="Kingdom"/>
55 <param name="database" value=""/>
56 <param name="mode" value="c_tmode"/>
57 <param name="lca_choice" value="source_tax"/>
58 <param name="threshold" value="1e-3"/>
59 <output name="output" ftype="tabular">
60 <assert_contents>
61 <has_text text=""/>
62 <has_line line=""/>
63 <has_line_matching expression=""/>
64 <has_n_columns n=""/>
65 <has_size value="" delta=""/>
66 </assert_contents>
67 </output>
68 </test>
69 </tests>
70 <help><![CDATA[
71 @HELP_HEADER@
72
73 Based on the lowest common ancestor (LCA) annotation
74 of each UniRef50/90 cluster, this tool infers approximate taxonomy
75 for unclassified features at a target level of resolution.
76
77 It will modify features of known genus/species to match
78 target level.
79 ]]></help>
80 <expand macro="citations"/>
81 </tool>