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comparison humann_renorm_table.xml @ 0:e3391ccf21a0 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 09:05:14 +0000
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1 <tool id="humann_renorm_table" name="Renormalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>a HUMAnN generated table</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_ontology"/>
7 <expand macro="requirements"/>
8 <expand macro="version"/>
9 <command detect_errors="exit_code"><![CDATA[
10 humann_renorm_table
11 --input '$input'
12 -o '$output'
13 --units '$units'
14 --mode '$mode'
15 --special '$special'
16 $update_snames
17 ]]></command>
18 <inputs>
19 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
20 <param argument="--units" type="select" label="Normalization scheme">
21 <option value="cpm" selected="true">Copies per million</option>
22 <option value="relab">Relative abundance</option>
23 </param>
24 <param argument="--mode" type="select" label="Normalization level">
25 <option value="community" selected="true">Normalization of all levels by community total</option>
26 <option value="levelwise">Normalization of all levels by levelwise total</option>
27 </param>
28 <param argument="--special" type='boolean' truevalue='y' falsevalue='n' checked="true" label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/>
29 <param argument="--update-snames" type='boolean' truevalue='--update-snames' falsevalue='' checked="true" label="Update '-RPK' in sample names to appropriate suffix?"/>
30 </inputs>
31 <outputs>
32 <data format="tabular" name="output"/>
33 </outputs>
34 <tests>
35 <test expect_num_outputs="1">
36 <param name="input" value="demo_pathabundance.tsv"/>
37 <param name="units" value="cpm"/>
38 <param name="mode" value="community"/>
39 <param name="special" value="n"/>
40 <param name="update_snames" value=""/>
41 <output name="output" ftype="tabular" file="cpm_community_renormalized_pathway_abundance.tsv">
42 <assert_contents>
43 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis" />
44 <has_text text="578694" />
45 </assert_contents>
46 </output>
47 </test>
48 <test expect_num_outputs="1">
49 <param name="input" value="demo_pathabundance.tsv"/>
50 <param name="units" value="relab"/>
51 <param name="mode" value="levelwise"/>
52 <param name="special" value="y"/>
53 <param name="update_snames" value=""/>
54 <output name="output" ftype="tabular" file="relab_levelwise_renormalized_pathway_abundance.tsv">
55 <assert_contents>
56 <has_text text="PWY-5423: oleoresin monoterpene volatiles biosynthesis|unclassified" />
57 <has_text text="0.630281" />
58 </assert_contents>
59 </output>
60 </test>
61 </tests>
62 <help><![CDATA[
63 @HELP_HEADER@
64
65 HUMAnN quantifies genes and pathways in units of RPKs (reads per kilobase). These account for gene length but not sample sequencing depth.
66 While there are some applications, e.g. strain profiling, where RPK units are superior to depth-normalized units, most of the
67 time a user will renormalize their samples prior to downstream analysis.
68
69 This tool provides the choice to normalize to relative abundance or copies per million (CPM) units. Both of these represent
70 "total sum scaling (TSS)"-style normalization: in the former case, each sample is constrained to sum to 1, whereas in the
71 latter case (CPMs) samples are constrained to sum to 1 million. Units out of 1 million are often more convenient for tables
72 with many, many features (such as genefamilies.tsv tables).
73
74 Note: CPM as used here does not refer to unnormalized COUNTS per million, but rather copies per million.
75 CPMs as used here are a generic analog of the TPM (transcript per million) unit in RNA-seq. You may wish to use the
76 abbreviation CoPM for added clarity.
77
78 By default, this tool normalizes all stratification levels to the sum of all community feature totals, but other options
79 (such as level-wise normalization) are supported. "Special" features (such as UNMAPPED) can be included or excluded in the
80 normalization process.
81 ]]></help>
82 <expand macro="citations"/>
83 </tool>