Mercurial > repos > bebatut > combine_metaphlan2_humann2
comparison combine_metaphlan2_humann2.xml @ 0:31394a0c0242 draft
planemo upload for repository https://github.com/asaim/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit e6bee6545960c2a1ae3ca3031ec74d7c26d0b0ce-dirty
author | bebatut |
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date | Fri, 15 Apr 2016 09:15:21 -0400 |
parents | |
children | e25efca0a49c |
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-1:000000000000 | 0:31394a0c0242 |
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1 <tool id="combine_metaphlan2_humann2" name="Combine MetaPhlAn2 and HUMAnN2 outputs" version="0.1.0"> | |
2 <description>to relate genus/species abundances and gene families/pathways abundances</description> | |
3 | |
4 <requirements> | |
5 </requirements> | |
6 | |
7 <stdio> | |
8 <exit_code range="1:" /> | |
9 <exit_code range=":-1" /> | |
10 </stdio> | |
11 | |
12 <version_command></version_command> | |
13 | |
14 <command><![CDATA[ | |
15 python $__tool_directory__/combine_metaphlan2_humann2.py | |
16 --metaphlan2_file $metaphlan2_file | |
17 --humann2_file $humann2_file | |
18 --type $type | |
19 | |
20 #if str($type) == 'gene_families' | |
21 --output_file $gene_families_output_file | |
22 #else | |
23 --output_file $pathway_output_file | |
24 #end if | |
25 ]]></command> | |
26 | |
27 <inputs> | |
28 <param name="metaphlan2_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn2 output" help="The MetaPhlAn2 output file contains relative abundance of clades at different taxonomic levels (--metaphlan2_file)"/> | |
29 | |
30 <param name="humann2_file" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN2 output" help="The HUMAnN2 output file contains relative abundance of gene families or pathways with corresponding taxonomic stratification (--humann2_file)"/> | |
31 | |
32 <param name='type' type="select" label="Type of characteristics in HUMAnN2 file" help="(--type)"> | |
33 <option value="gene_families" selected="true">Gene families</option> | |
34 <option value="pathways">Pathways</option> | |
35 </param> | |
36 </inputs> | |
37 | |
38 <outputs> | |
39 <data name="gene_families_output_file" format="tabular" | |
40 label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" > | |
41 <filter>type=="gene_families"</filter> | |
42 </data> | |
43 <data name="pathway_output_file" format="tabular" | |
44 label="${tool.name} on ${on_string}: Pathway abundances related to genus/species abundances" > | |
45 <filter>type=="pathways"</filter> | |
46 </data> | |
47 </outputs> | |
48 | |
49 <tests> | |
50 <test> | |
51 <param name="metaphlan2_file" value="metaphlan2_input.txt"/> | |
52 <param name="humann2_file" value="humann2_gene_families_input.tabular"/> | |
53 <param name='type' value="gene_families"/> | |
54 <output name="gene_families_output_file" file="gene_families_output.tabular"/> | |
55 </test> | |
56 <test> | |
57 <param name="metaphlan2_file" value="metaphlan2_input.txt"/> | |
58 <param name="humann2_file" value="humann2_pathways_input.tabular"/> | |
59 <param name='type' value="pathways"/> | |
60 <output name="pathway_output_file" file="pathways_output.tabular"/> | |
61 </test> | |
62 </tests> | |
63 | |
64 <help><![CDATA[ | |
65 **What it does** | |
66 | |
67 This tool combine MetaPhlAn2 outputs and HUMANnN2 outputs. | |
68 | |
69 For each gene families/pathways and the corresponding taxonomic stratification, you get relative abundance of this gene family/pathway and the relative abundance of corresponding species and genus. | |
70 ]]></help> | |
71 | |
72 <citations> | |
73 </citations> | |
74 </tool> |