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comparison humann2_join_tables.xml @ 0:e3c88925060e draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b'f126d56aa160b10437d9dabf5c9e32fd4569fee6\n'-dirty
author bebatut
date Mon, 20 Feb 2017 11:40:32 -0500
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1 <tool id="humann2_join_tables" name="Join" version="@WRAPPER_VERSION@.0">
2 <description>HUMAnN2 generated tables</description>
3
4 <macros>
5 <import>humann2_macros.xml</import>
6 </macros>
7
8 <expand macro="requirements"/>
9 <expand macro="stdio"/>
10
11 <version_command>
12 <![CDATA[
13 humann2_join_tables --version
14 ]]>
15 </version_command>
16
17 <command><![CDATA[
18 mkdir tmp_dir
19
20 &&
21
22 #for $table in $input_tables
23 cp '$table.input_table' 'tmp_dir' &&
24 #end for
25
26 humann2_join_tables
27 -i 'tmp_dir'
28 -o '$joined_table'
29 ]]></command>
30
31 <inputs>
32 <repeat name="input_tables" title="Gene/pathway tables to join">
33 <param name="input_table" type="data" format="tsv,tabular" multiple="true" label="Gene/pathway table" help=""/>
34 </repeat>
35 </inputs>
36
37 <outputs>
38 <data format="tsv" name="joined_table" label="${tool.name} on ${on_string}: Joined table" />
39 </outputs>
40
41 <tests>
42 <test>
43 <param name="input_tables_0|input_table" value="demo_pathabundance.tsv"/>
44 <param name="input_tables_1|input_table" value="demo_pathcoverage.tsv"/>
45 <output name="joined_table">
46 <assert_contents>
47 <has_text text="PWY490-3: nitrate reduction VI (assimilatory)|unclassified" />
48 <has_text text="PWY-1269: CMP-3-deoxy-D-manno-octulosonate biosynthesis I" />
49 <has_text text="VALSYN-PWY: L-valine biosynthesis" />
50 <has_text text="UNINTEGRATED|g__Bacteroides.s__Bacteroides_vulgatus" />
51 </assert_contents>
52 </output>
53 </test>
54 </tests>
55
56 <help><![CDATA[
57 **What it does**
58 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>`_.
59
60 Join HUMAnN2 tables is a tool to join gene or pathway tables of multiple samples into a single table.
61 ]]></help>
62
63 <expand macro="citations"/>
64 </tool>