Mercurial > repos > iuc > humann2_unpack_pathways

comparison generate_test_data @ 0:d2e4fee96dd1 draft

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planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
author iuc
date Tue, 01 Aug 2017 07:56:57 -0400
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-1:000000000000 0:d2e4fee96dd1
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_associate
52 humann2_associate \
53 --input 'test-data/hmp_pathabund.txt' \
54 --focal-metadatum 'STSite' \
55 --last-metadatum 'STSite' \
56 --focal-type 'categorical' \
57 --fdr '0.2' \
58 --output 'test-data/associate_output.txt'
59
60 # humann2_barplot
61 humann2_barplot \
62 --input 'test-data/hmp_pathabund.txt' \
63 --focal-feature ANAGLYCOLYSIS-PWY \
64 --sort none \
65 --last-metadatum STSite \
66 --focal-metadatum STSite \
67 --scaling none \
68 --width 5 \
69 --dimensions 8 4 \
70 --output test-data/barplot1.png
71
72 humann2_barplot \
73 --input 'test-data/hmp_pathabund.txt' \
74 --focal-feature ANAGLYCOLYSIS-PWY \
75 --sort sum \
76 --last-metadatum STSite \
77 --focal-metadatum STSite \
78 --scaling pseudolog \
79 --width 5 \
80 --dimensions 8 4 \
81 --output test-data/barplot2.pdf
82
83 humann2_barplot \
84 --input 'test-data/hmp_pathabund.txt' \
85 --focal-feature ANAGLYCOLYSIS-PWY \
86 --sort metadata \
87 --last-metadatum STSite \
88 --focal-metadatum STSite \
89 --exclude-unclassified \
90 --scaling none \
91 --as-genera \
92 --grid \
93 --remove-zeroes \
94 --width 5 \
95 --dimensions 8 4 \
96 --output test-data/barplot3.svg
97
98 humann2_barplot \
99 --input 'test-data/hmp_pathabund.txt' \
100 --focal-feature ANAGLYCOLYSIS-PWY \
101 --top-strata 12 \
102 --sort sum \
103 --last-metadatum STSite \
104 --focal-metadatum STSite \
105 --exclude-unclassified \
106 --scaling normalize \
107 --width 5 \
108 --dimensions 8 4 \
109 --output test-data/barplot4.eps
110
111 # humann2_regroup_table
112 humann2_regroup_table \
113 --input 'test-data/demo_genefamilies.tsv' \
114 -o 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
115 --function 'sum' \
116 --groups 'uniref90_infogo1000' \
117 --ungrouped 'Y' \
118 --protected 'Y'
119
120 humann2_regroup_table \
121 --input 'test-data/demo_genefamilies.tsv' \
122 -o 'test-data/regrouped_gene_families_to_ko.tsv' \
123 --function 'mean' \
124 --groups 'uniref90_ko' \
125 --ungrouped 'Y' \
126 --protected 'Y'
127
128 humann2_regroup_table \
129 --input 'test-data/demo_genefamilies.tsv' \
130 -o 'test-data/regrouped_gene_families_to_rxn.tsv' \
131 --function 'sum' \
132 --groups 'uniref90_rxn' \
133 --ungrouped 'Y' \
134 --protected 'Y'
135
136 # humann2_renorm_table
137 humann2_renorm_table \
138 --input 'test-data/demo_pathabundance.tsv' \
139 -o 'test-data/cpm_community_renormalized_pathway_abundance.tsv' \
140 --units 'cpm' \
141 --mode 'community' \
142 --special 'n'
143
144 humann2_renorm_table \
145 --input 'test-data/demo_pathabundance.tsv' \
146 -o 'test-data/relab_levelwise_renormalized_pathway_abundance.tsv' \
147 --units 'relab' \
148 --mode 'levelwise' \
149 --special 'y'
150
151 # humann2_join_tables
152 mkdir join_table_tmp_dir
153 cp 'test-data/demo_pathabundance.tsv' join_table_tmp_dir
154 cp 'test-data/demo_pathcoverage.tsv' join_table_tmp_dir
155 humann2_join_tables \
156 -i 'join_table_tmp_dir' \
157 -o 'test-data/joined_pathway_coverage_abundance.tsv'
158
159 # humann2_merge_abundance_tables
160 humann2_merge_abundance_tables \
161 --input-genes 'test-data/demo_genefamilies.tsv' \
162 --input-pathways 'test-data/demo_pathabundance.tsv' \
163 -o 'test-data/merged_gene_families_pathways_abundances.tsv'
164
165 # humann2_reduce_table
166 humann2_reduce_table \
167 --input 'test-data/demo_genefamilies.tsv' \
168 -o 'test-data/max_reduced_gene_family_abundance.tsv' \
169 --function 'max' \
170 --sort-by 'name'
171
172 # humann2_rename_table
173 humann2_rename_table \
174 --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
175 --names 'infogo1000' \
176 -o 'test-data/renamed_info1000.tsv'
177
178 humann2_rename_table \
179 --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
180 --custom 'test-data/rename_mapping' \
181 -o 'test-data/renamed_mapping_info1000.tsv'
182
183 # humann2_rna_dna_norm
184 humann2_rna_dna_norm \
185 --input_dna 'test-data/rna_dna_norm-dna.txt' \
186 --input_rna 'test-data/rna_dna_norm-rna.txt' \
187 --output_basename 'results1' \
188 --method 'laplace'
189
190 humann2_rna_dna_norm \
191 --input_dna 'test-data/rna_dna_norm-dna.txt' \
192 --input_rna 'test-data/rna_dna_norm-rna.txt' \
193 --output_basename 'results2' \
194 --method 'witten_bell' \
195 --log_transform \
196 --log_base '2'
197
198 # humann2_split_stratified_table
199 humann2_split_stratified_table \
200 --input 'test-data/demo_genefamilies.tsv' \
201 --output 'split_stratified_table'
202
203 # humann2_split_table
204 mkdir split_table_tmp_dir
205 humann2_split_table \
206 --input 'test-data/joined_pathway_coverage_abundance.tsv' \
207 -o 'split_table_tmp_dir'
208 cp 'split_table_tmp_dir/demo_Abundance.tsv' 'test-data/'
209 cp 'split_table_tmp_dir/demo_Coverage.tsv' 'test-data/'
210
211 # humann2_strain_profiler
212 humann2_strain_profiler \
213 --input 'test-data/strain_profiler-input.txt' \
214 --critical_mean '1' \
215 --critical_count '2' \
216 --pinterval '1e-10' '1' \
217 --critical_samples '2'
218
219 # humann2_unpack_pathways
220 humann2_unpack_pathways \
221 --input-genes 'test-data/demo_genefamilies.tsv' \
222 --input-pathways 'test-data/demo_pathabundance.tsv' \
223 --output unpack1
224
225 humann2_unpack_pathways \
226 --input-genes 'test-data/demo_genefamilies.tsv' \
227 --input-pathways 'test-data/demo_pathabundance.tsv' \
228 --remove-taxonomy \
229 --output unpack2