Mercurial > repos > iuc > humann2_regroup_table

comparison generate_test_data @ 0:a1747df2bc21 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 12:38:02 -0400
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children 1d141730ec69
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-1:000000000000 0:a1747df2bc21
1 #/usr/bin/env bash
2
3 # humann2
4 humann2 \
5 --input 'test-data/input_sequences.fasta' \
6 -o 'humann2_output' \
7 --annotation-gene-index 8 \
8 --taxonomic-profile 'test-data/taxonomic_profile.tabular' \
9 --metaphlan-options="-t rel_ab" \
10 --nucleotide-database 'test-data/' \
11 --protein-database 'test-data/' \
12 --evalue '1' \
13 --search-mode 'uniref50' \
14 --prescreen-threshold '0.01' \
15 --identity-threshold '50' \
16 --translated-subject-coverage-threshold '50' \
17 --translated-query-coverage-threshold '50' \
18 --translated-alignment 'diamond' \
19 --xipe 'off' \
20 --minpath 'on' \
21 --pick-frames 'on' \
22 --gap-fill 'off' \
23 --output-format 'tsv' \
24 --output-max-decimals '10' \
25 --output-basename 'humann2' \
26 --pathways 'metacyc'
27
28 humann2 \
29 --input 'test-data/input_sequences.fasta' \
30 -o 'humann2_output' \
31 --annotation-gene-index 8 \
32 --metaphlan-options="-t rel_ab" \
33 --nucleotide-database 'test-data/' \
34 --protein-database 'test-data/' \
35 --evalue '1' \
36 --search-mode 'uniref90' \
37 --prescreen-threshold '0.01' \
38 --identity-threshold '50' \
39 --translated-subject-coverage-threshold '50' \
40 --translated-query-coverage-threshold '50' \
41 --translated-alignment 'rapsearch' \
42 --xipe 'off' \
43 --minpath 'on' \
44 --pick-frames 'on' \
45 --gap-fill 'off' \
46 --output-format 'tsv' \
47 --output-max-decimals '10' \
48 --output-basename 'humann2' \
49 --pathways 'unipathway'
50
51 # humann2_regroup_table
52 humann2_regroup_table \
53 --input 'test-data/demo_genefamilies.tsv' \
54 -o 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
55 --function 'sum' \
56 --groups 'uniref90_infogo1000' \
57 --ungrouped 'Y' \
58 --protected 'Y'
59
60 humann2_regroup_table \
61 --input 'test-data/demo_genefamilies.tsv' \
62 -o 'test-data/regrouped_gene_families_to_ko.tsv' \
63 --function 'mean' \
64 --groups 'uniref90_ko' \
65 --ungrouped 'Y' \
66 --protected 'Y'
67
68 humann2_regroup_table \
69 --input 'test-data/demo_genefamilies.tsv' \
70 -o 'test-data/regrouped_gene_families_to_rxn.tsv' \
71 --function 'sum' \
72 --groups 'uniref90_rxn' \
73 --ungrouped 'Y' \
74 --protected 'Y'
75
76 # humann2_renorm_table
77 humann2_renorm_table \
78 --input 'test-data/demo_pathabundance.tsv' \
79 -o 'test-data/cpm_community_renormalized_pathway_abundance.tsv' \
80 --units 'cpm' \
81 --mode 'community' \
82 --special 'n'
83
84 humann2_renorm_table \
85 --input 'test-data/demo_pathabundance.tsv' \
86 -o 'test-data/relab_levelwise_renormalized_pathway_abundance.tsv' \
87 --units 'relab' \
88 --mode 'levelwise' \
89 --special 'y'
90
91 # humann2_join_tables
92 mkdir join_table_tmp_dir
93 cp 'test-data/demo_pathabundance.tsv' join_table_tmp_dir
94 cp 'test-data/demo_pathcoverage.tsv' join_table_tmp_dir
95 humann2_join_tables \
96 -i 'join_table_tmp_dir' \
97 -o 'test-data/joined_pathway_coverage_abundance.tsv'
98
99 # humann2_merge_abundance_tables
100 humann2_merge_abundance_tables \
101 --input-genes 'test-data/demo_genefamilies.tsv' \
102 --input-pathways 'test-data/demo_pathabundance.tsv' \
103 -o 'test-data/merged_gene_families_pathways_abundances.tsv'
104
105 # humann2_reduce_table
106 humann2_reduce_table \
107 --input 'test-data/demo_genefamilies.tsv' \
108 -o 'test-data/max_reduced_gene_family_abundance.tsv' \
109 --function 'max' \
110 --sort-by 'name'
111
112 # humann2_rename_table
113 humann2_rename_table \
114 --input 'test-data/demo_genefamilies.tsv' \
115 -o 'test-data/renamed_genefamilies.tsv' \
116 --names 'metacyc-pwy'
117
118 # humann2_split_table
119 mkdir split_table_tmp_dir
120 humann2_split_table \
121 --input 'test-data/joined_pathway_coverage_abundance.tsv' \
122 -o 'split_table_tmp_dir'
123 cp 'split_table_tmp_dir/demo_Abundance.tsv' 'test-data/'
124 cp 'split_table_tmp_dir/demo_Coverage.tsv' 'test-data/'