Mercurial > repos > bebatut > combine_metaphlan2_humann2
comparison combine_metaphlan_humann.xml @ 3:01ac9954c27f draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/combine_metaphlan2_humann2 commit b84cbcbffa25c55acd1a31df76e4a4f78772cbd7
author | bgruening |
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date | Thu, 20 Jul 2023 10:07:12 +0000 |
parents | |
children | 662a334004b4 |
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2:fdfb35745104 | 3:01ac9954c27f |
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1 <tool id="combine_metaphlan_humann" name="Combine MetaPhlAn and HUMAnN outputs" version="0.3.0" profile="22.01"> | |
2 <description>to relate genus/species abundances and gene families/pathways abundances</description> | |
3 <requirements> | |
4 <requirement type="package" version="3.10">python</requirement> | |
5 </requirements> | |
6 <version_command></version_command> | |
7 <command detect_errors="aggressive"><![CDATA[ | |
8 python '$__tool_directory__/combine_metaphlan_humann.py' | |
9 --metaphlan_fp '$metaphlan_file' | |
10 --humann_fp '$humann_file' | |
11 --type '$type' | |
12 | |
13 #if str($type) == 'gene_families' | |
14 --output_fp '$gene_families_output_file' | |
15 #else | |
16 --output_fp '$pathway_output_file' | |
17 #end if | |
18 ]]></command> | |
19 <inputs> | |
20 <param argument="--metaphlan_file" format="txt,tabular" type="data" label="Input file corresponding to MetaPhlAn output" help="The MetaPhlAn output file contains relative abundance of clades at different taxonomic levels"/> | |
21 <param argument="--humann_file" format="txt,tabular" type="data" label="Input file corresponding to HUMAnN output" help="The HUMAnN output file contains relative abundance of gene families or pathways with corresponding taxonomic stratification"/> | |
22 <param argument='--type' type="select" label="Type of characteristics in HUMAnN file"> | |
23 <option value="gene_families" selected="true">Gene families</option> | |
24 <option value="pathways">Pathways</option> | |
25 </param> | |
26 </inputs> | |
27 <outputs> | |
28 <data name="gene_families_output_file" format="tabular" | |
29 label="${tool.name} on ${on_string}: Gene family abundances related to genus/species abundances" > | |
30 <filter>type=="gene_families"</filter> | |
31 </data> | |
32 <data name="pathway_output_file" format="tabular" | |
33 label="${tool.name} on ${on_string}: Pathway abundances related to genus/species abundances" > | |
34 <filter>type=="pathways"</filter> | |
35 </data> | |
36 </outputs> | |
37 <tests> | |
38 <!-- Using the output of old (i.e. v2) Humann and metaphlan --> | |
39 <test expect_num_outputs="1"> | |
40 <param name="metaphlan_file" value="metaphlan2_input.txt"/> | |
41 <param name="humann_file" value="humann2_gene_families_input.tabular"/> | |
42 <param name='type' value="gene_families"/> | |
43 <output name="gene_families_output_file"> | |
44 <assert_contents> | |
45 <has_n_columns n="8"/> | |
46 <has_n_lines n="3043"/> | |
47 <has_text text="Staphylococcus_epidermidis"/> | |
48 <has_text text="Putative transposon Tn552 DNA invertase bin3"/> | |
49 <has_size value="374787"/> | |
50 </assert_contents> | |
51 </output> | |
52 </test> | |
53 <test expect_num_outputs="1"> | |
54 <param name="metaphlan_file" value="metaphlan2_input.txt"/> | |
55 <param name="humann_file" value="humann2_pathways_input.tabular"/> | |
56 <param name='type' value="pathways"/> | |
57 <output name="pathway_output_file"> | |
58 <assert_contents> | |
59 <has_n_columns n="8"/> | |
60 <has_n_lines n="1533"/> | |
61 <has_text text="Rhodobacter_sphaeroides"/> | |
62 <has_text text="superpathway of acetyl CoA biosynthesis"/> | |
63 <has_size value="186363"/> | |
64 </assert_contents> | |
65 </output> | |
66 </test> | |
67 | |
68 <!-- Using the output of v3 Humann and v4 metaphlan --> | |
69 <test expect_num_outputs="1"> | |
70 <param name="metaphlan_file" value="metaphlan4_input.txt"/> | |
71 <param name="humann_file" value="humann36_gene_families_input.tabular"/> | |
72 <param name='type' value="gene_families"/> | |
73 <output name="gene_families_output_file"> | |
74 <assert_contents> | |
75 <has_n_columns n="8"/> | |
76 <has_n_lines n="2242"/> | |
77 <has_text text="Acetivibrio_thermocellus"/> | |
78 <has_size value="213828"/> | |
79 </assert_contents> | |
80 </output> | |
81 </test> | |
82 <test expect_num_outputs="1"> | |
83 <param name="metaphlan_file" value="metaphlan4_input.txt"/> | |
84 <param name="humann_file" value="humann36_pathways_input.tabular"/> | |
85 <param name='type' value="pathways"/> | |
86 <output name="pathway_output_file"> | |
87 <assert_contents> | |
88 <has_n_columns n="8"/> | |
89 <has_n_lines n="49"/> | |
90 <has_text text="Acetivibrio_thermocellus"/> | |
91 <has_text text="preQ0 biosynthesis"/> | |
92 <has_size value="6102"/> | |
93 </assert_contents> | |
94 </output> | |
95 </test> | |
96 </tests> | |
97 <help><![CDATA[ | |
98 **What it does** | |
99 | |
100 This tool combine MetaPhlAn outputs and HUMANnN outputs. | |
101 | |
102 For each gene families/pathways and the corresponding taxonomic stratification, | |
103 you get relative abundance of this gene family/pathway and the relative abundance | |
104 of corresponding species and genus. | |
105 ]]></help> | |
106 <citations> | |
107 <citation type="doi">10.7554/eLife.65088</citation> | |
108 </citations> | |
109 </tool> |