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comparison humann2_reduce_table.xml @ 0:947012405a6e draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit dd6f3fda4d992efa4a91ee0823ecc3af8a9532d3-dirty
author bebatut
date Thu, 17 Dec 2015 08:58:05 -0500
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1 <tool id="humann2_reduce_table" name="Reduce HUMAnN2 table" version="0.1.0">
2 <description></description>
3
4 <requirements>
5 <requirement type="package" version="2.2.4">bowtie2</requirement>
6 <requirement type="package" version="2.0">metaphlan2</requirement>
7 <requirement type="package" version="0.6.13">diamond</requirement>
8 <requirement type="package" version="2.0">humann2</requirement>
9 </requirements>
10
11 <stdio>
12 <exit_code range="1:" />
13 </stdio>
14
15 <version_command>
16 <![CDATA[
17 humann2_reduce_table --version
18 ]]>
19 </version_command>
20
21 <command><![CDATA[
22 humann2_reduce_table
23 -i $input_table
24 -o $output_table
25 --function $function
26 --sort-by $sort
27 ]]></command>
28
29 <inputs>
30 <param name="input_table" type="data" format="tsv" label="Gene/pathway
31 table" help=""/>
32
33 <param name="function" type="select" label="Function to apply" help="(--function)">
34 <option value="max" selected="true">Max</option>
35 <option value="sum">Sum</option>
36 <option value="mean">Mean</option>
37 <option value="min">Min</option>
38 </param>
39
40 <param name="sort" type="select" label="How to sort the output" help="(--sort-by)">
41 <option value="name" selected="true">Name</option>
42 <option value="value">value</option>
43 <option value="level">level</option>
44 </param>
45 </inputs>
46
47 <outputs>
48 <data format="tsv" name="output_table" label="Reduced table for
49 ${on_string} (HUMAnN2)" />
50 </outputs>
51
52 <tests>
53 <test>
54 <param name="input_table" value="humann2_sam_pathcoverage.tsv"/>
55 <param name="function" value="max"/>
56 <param name="sort" value="name"/>
57 <output name="output_table" file="humann2_sam_reduced_pathcoverage.tsv"/>
58 </test>
59 </tests>
60
61 <help><![CDATA[
62 **What it does**
63
64 Reduce HUMAnN2 table is a tool to reduce the table given a function (max, sum, mean or min).
65
66 HUMAnN is a pipeline for efficiently and accuretly profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data. `Read more about the tool <http://huttenhower.sph.harvard.edu/humann2/manual>`_.
67
68 ]]></help>
69
70 <citations>
71 </citations>
72 </tool>