Mercurial > repos > iuc > humann2_rna_dna_norm

comparison humann2_rna_dna_norm.xml @ 0:c8ef30c8451d draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author iuc
date Tue, 01 Aug 2017 07:56:14 -0400
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1 <tool id="humann2_rna_dna_norm" name="Normalize" version="@WRAPPER_VERSION@.0">
2 <description> combined meta'omic sequencing data</description>
3 <macros>
4 <import>humann2_macros.xml</import>
5 </macros>
6 <expand macro="requirements"/>
7 <expand macro="version"/>
8 <command detect_errors="exit_code"><![CDATA[
9 humann2_rna_dna_norm
10 --input_dna '$input_dna'
11 --input_rna '$input_rna'
12 --output_basename 'results'
13 --method '$method'
14 #if $log.log_transform == 'yes'
15 --log_transform
16 --log_base $log.log_base
17 #end if
18 ]]></command>
19 <inputs>
20 <param argument="--input_dna" type="data" format="tsv,tabular,biom1" label="Original DNA output table"/>
21 <param argument="--input_rna" type="data" format="tsv,tabular,biom1" label="Original RNA output table"/>
22 <param argument="--method" type="select" label="Choice of smoothing method">
23 <option value="laplace">Laplace</option>
24 <option value="witten_bell">Witten-Bell</option>
25 </param>
26 <conditional name="log">
27 <param argument="--log_transform" type="select" label="Report log-transformed relative expression values?">
28 <option value="yes">Yes</option>
29 <option value="no">No</option>
30 </param>
31 <when value="yes">
32 <param argument="--log_base" type="integer" value="2" label="Base for log transformation"/>
33 </when>
34 <when value="no"/>
35 </conditional>
36 </inputs>
37 <outputs>
38 <data format="tsv" name="results-relative_expression" from_work_dir="results-relative_expression.tsv" label="${tool.name} on ${on_string}: normalized RNA"/>
39 <data format="tsv" name="results-smoothed_dna" from_work_dir="results-smoothed_dna.tsv" label="${tool.name} on ${on_string}: smoothed DNA"/>
40 <data format="tsv" name="results-smoothed_rna" from_work_dir="results-smoothed_rna.tsv" label="${tool.name} on ${on_string}: smoothed RNA"/>
41 </outputs>
42 <tests>
43 <test>
44 <param name="input_dna" value="rna_dna_norm-dna.txt"/>
45 <param name="input_rna" value="rna_dna_norm-rna.txt"/>
46 <param name="method" value="laplace"/>
47 <conditional name="log">
48 <param name="log_transform" value="no"/>
49 </conditional>
50 <output name="results-relative_expression" md5="193000abf357cb14f70273ba6cd5f095"/>
51 <output name="results-smoothed_dna" md5="3767aa13988a4dca40a07cb6970bcc60"/>
52 <output name="results-smoothed_rna" md5="8b1bcb819c31ef0ba5ab4975582bfcf7"/>
53 </test>
54 <test>
55 <param name="input_dna" value="rna_dna_norm-dna.txt"/>
56 <param name="input_rna" value="rna_dna_norm-rna.txt"/>
57 <param name="method" value="witten_bell"/>
58 <conditional name="log">
59 <param name="log_transform" value="yes"/>
60 <param name="log_base" value="2"/>
61 </conditional>
62 <output name="results-relative_expression" md5="3064e6377c074c6e6e9cf7fdfd466ec9"/>
63 <output name="results-smoothed_dna" md5="3a1203c0986d79e9cb4ac0e3a4a89f4e"/>
64 <output name="results-smoothed_rna" md5="1038b44e52b95a867dc6341b4dd91697"/>
65 </test>
66 </tests>
67 <help><![CDATA[
68 @HELP_HEADER@
69
70 Given a DNA table and a RNA table, produce smoothed RNA and DNA values as well as relative expression values. "Smoothing" means substituting a small value in place of a zero or missing value. 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.)
71 ]]></help>
72 <expand macro="citations"/>
73 </tool>