Mercurial > repos > iuc > humann2_reduce_table

comparison generate_test_data @ 1:d020ce7b0e4c 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 07:57:49 -0400
parents e795ba0b91f4
children
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0:e795ba0b91f4 1:d020ce7b0e4c
46 --output-format 'tsv' \ 46 --output-format 'tsv' \
47 --output-max-decimals '10' \ 47 --output-max-decimals '10' \
48 --output-basename 'humann2' \ 48 --output-basename 'humann2' \
49 --pathways 'unipathway' 49 --pathways 'unipathway'
50 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
51 # humann2_regroup_table 111 # humann2_regroup_table
52 humann2_regroup_table \ 112 humann2_regroup_table \
53 --input 'test-data/demo_genefamilies.tsv' \ 113 --input 'test-data/demo_genefamilies.tsv' \
54 -o 'test-data/regrouped_gene_families_to_infogo1000.tsv' \ 114 -o 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
55 --function 'sum' \ 115 --function 'sum' \
109 --function 'max' \ 169 --function 'max' \
110 --sort-by 'name' 170 --sort-by 'name'
111 171
112 # humann2_rename_table 172 # humann2_rename_table
113 humann2_rename_table \ 173 humann2_rename_table \
114 --input 'test-data/demo_genefamilies.tsv' \ 174 --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
115 -o 'test-data/renamed_genefamilies.tsv' \ 175 --names 'infogo1000' \
116 --names 'metacyc-pwy' 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'
117 202
118 # humann2_split_table 203 # humann2_split_table
119 mkdir split_table_tmp_dir 204 mkdir split_table_tmp_dir
120 humann2_split_table \ 205 humann2_split_table \
121 --input 'test-data/joined_pathway_coverage_abundance.tsv' \ 206 --input 'test-data/joined_pathway_coverage_abundance.tsv' \
122 -o 'split_table_tmp_dir' 207 -o 'split_table_tmp_dir'
123 cp 'split_table_tmp_dir/demo_Abundance.tsv' 'test-data/' 208 cp 'split_table_tmp_dir/demo_Abundance.tsv' 'test-data/'
124 cp 'split_table_tmp_dir/demo_Coverage.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