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comparison humann2_renorm_table.xml @ 0:ba4dfbdc1295 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
author iuc
date Mon, 13 Mar 2017 12:38:56 -0400
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1 <tool id="humann2_renorm_table" name="Renormalize" version="@WRAPPER_VERSION@.0">
2 <description>a HUMAnN2 generated table</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_renorm_table
10 --input '$input'
11 -o '$output_table'
12 --units '$units'
13 --mode '$mode'
14 --special '$special'
15 ]]></command>
16 <inputs>
17 <param argument="--input" type="data" format="tsv,tabular" label="Gene/pathway table"/>
18 <param argument="--units" type="select" label="Normalization scheme">
19 <option value="cpm" selected="true">Copies per million</option>
20 <option value="relab">Relative abundance</option>
21 </param>
22 <param argument="--mode" type="select" label="Normalization level">
23 <option value="community" selected="true">Normalization of all levels by community total</option>
24 <option value="levelwise">Normalization of all levels by levelwise total</option>
25 </param>
26 <param argument="--special" type='boolean' checked="true" truevalue='y' falsevalue='n' label="Include the special features UNMAPPED, UNINTEGRATED, and UNGROUPED?"/>
27 </inputs>
28 <outputs>
29 <data format="tsv" name="output_table" label="${tool.name} on ${on_string}: Normalized table" />
30 </outputs>
31 <tests>
32 <test>
33 <param name="input" value="demo_pathabundance.tsv"/>
34 <param name="units" value="cpm"/>
35 <param name="mode" value="community"/>
36 <param name="special" value="n"/>
37 <output name="output_table" file="cpm_community_renormalized_pathway_abundance.tsv"/>
38 </test>
39 <test>
40 <param name="input" value="demo_pathabundance.tsv"/>
41 <param name="units" value="relab"/>
42 <param name="mode" value="levelwise"/>
43 <param name="special" value="y"/>
44 <output name="output_table" file="relab_levelwise_renormalized_pathway_abundance.tsv"/>
45 </test>
46 </tests>
47 <help><![CDATA[
48 @HELP_HEADER@
49
50 Renorm HUMAnN2 table is a tool to renormalize a table, either in copies per million or in relative abundance. Each level of a stratified table will be normalized using the desired scheme.
51
52 ]]></help>
53 <expand macro="citations"/>
54 </tool>