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comparison humann_rna_dna_norm.xml @ 0:ec422794133f 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 09:01:24 +0000
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1 <tool id="humann_rna_dna_norm" name="Normalize" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description> combined meta'omic sequencing data</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_rna_dna_norm
11 --input_dna '$input_dna'
12 --input_rna '$input_rna'
13 --output_basename 'results'
14 --method '$method'
15 #if $log.log_transform == 'yes'
16 --log_transform
17 --log_base $log.log_base
18 #end if
19 ]]></command>
20 <inputs>
21 <param argument="--input_dna" type="data" format="tsv,tabular,biom1" label="Original DNA output table"/>
22 <param argument="--input_rna" type="data" format="tsv,tabular,biom1" label="Original RNA output table"/>
23 <param argument="--method" type="select" label="Choice of smoothing method">
24 <option value="laplace">Laplace</option>
25 <option value="witten_bell">Witten-Bell</option>
26 </param>
27 <conditional name="log">
28 <param argument="--log_transform" type="select" label="Report log-transformed relative expression values?">
29 <option value="yes">Yes</option>
30 <option value="no">No</option>
31 </param>
32 <when value="yes">
33 <param argument="--log_base" type="integer" value="2" label="Base for log transformation"/>
34 </when>
35 <when value="no"/>
36 </conditional>
37 </inputs>
38 <outputs>
39 <data format="tabular" name="relative_expression" from_work_dir="results-relative_expression.tsv" label="${tool.name} on ${on_string}: Normalized RNA"/>
40 <data format="tabular" name="smoothed_dna" from_work_dir="results-smoothed_dna.tsv" label="${tool.name} on ${on_string}: Smoothed DNA"/>
41 <data format="tabular" name="smoothed_rna" from_work_dir="results-smoothed_rna.tsv" label="${tool.name} on ${on_string}: Smoothed RNA"/>
42 </outputs>
43 <tests>
44 <test expect_num_outputs="3">
45 <param name="input_dna" value="rna_dna_norm-dna.txt"/>
46 <param name="input_rna" value="rna_dna_norm-rna.txt"/>
47 <param name="method" value="laplace"/>
48 <conditional name="log">
49 <param name="log_transform" value="no"/>
50 </conditional>
51 <output name="relative_expression" ftype="tabular">
52 <assert_contents>
53 <has_text text="A|1"/>
54 <has_text text="0.285714"/>
55 <has_n_columns n="3"/>
56 </assert_contents>
57 </output>
58 <output name="smoothed_dna" ftype="tabular">
59 <assert_contents>
60 <has_text text="A|1"/>
61 <has_text text="13"/>
62 <has_n_columns n="3"/>
63 </assert_contents>
64 </output>
65 <output name="smoothed_rna" ftype="tabular">
66 <assert_contents>
67 <has_text text="A|1"/>
68 <has_text text="62"/>
69 <has_n_columns n="3"/>
70 </assert_contents>
71 </output>
72 </test>
73 <test expect_num_outputs="3">
74 <param name="input_dna" value="rna_dna_norm-dna.txt"/>
75 <param name="input_rna" value="rna_dna_norm-rna.txt"/>
76 <param name="method" value="witten_bell"/>
77 <conditional name="log">
78 <param name="log_transform" value="yes"/>
79 <param name="log_base" value="2"/>
80 </conditional>
81 <output name="relative_expression" ftype="tabular">
82 <assert_contents>
83 <has_text text="A|1"/>
84 <has_text text="0.118644"/>
85 <has_n_columns n="3"/>
86 </assert_contents>
87 </output>
88 <output name="smoothed_dna" ftype="tabular">
89 <assert_contents>
90 <has_text text="A|1"/>
91 <has_text text="9.24"/>
92 <has_n_columns n="3"/>
93 </assert_contents>
94 </output>
95 <output name="smoothed_rna" ftype="tabular">
96 <assert_contents>
97 <has_text text="A|1"/>
98 <has_text text="39.4545"/>
99 <has_n_columns n="3"/>
100 </assert_contents>
101 </output>
102 </test>
103 </tests>
104 <help><![CDATA[
105 @HELP_HEADER@
106
107 Given a DNA table and a RNA table, this tool produces smoothed RNA and DNA values as well as relative expression values.
108
109 "Smoothing" means substituting a small value in place of a zero or missing value.
110 The default method used is "Laplace" (pseudocount) scaling, where the pseudocount is the sample-specific minimum non-zero value (Witten-Bell smoothing is also implemented.)
111
112 The DNA and RNA columns must be 1:1 and in the same order.
113
114 If working with stratified data, smoothing is carried out on the stratified values and then community totals are recomputed.
115 ]]></help>
116 <expand macro="citations"/>
117 </tool>