Mercurial > repos > iuc > humann2_unpack_pathways

annotate generate_test_data @ 4:3115a530686e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
author iuc
date Fri, 05 Feb 2021 18:23:16 +0000
parents d2e4fee96dd1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
1 #/usr/bin/env bash
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
2
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
3 # humann2
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
4 humann2 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
5 --input 'test-data/input_sequences.fasta' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
6 -o 'humann2_output' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
7 --annotation-gene-index 8 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
8 --taxonomic-profile 'test-data/taxonomic_profile.tabular' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
9 --metaphlan-options="-t rel_ab" \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
10 --nucleotide-database 'test-data/' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
11 --protein-database 'test-data/' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
12 --evalue '1' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
13 --search-mode 'uniref50' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
14 --prescreen-threshold '0.01' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
15 --identity-threshold '50' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
16 --translated-subject-coverage-threshold '50' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
17 --translated-query-coverage-threshold '50' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
18 --translated-alignment 'diamond' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
19 --xipe 'off' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
20 --minpath 'on' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
21 --pick-frames 'on' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
22 --gap-fill 'off' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
23 --output-format 'tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
24 --output-max-decimals '10' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
25 --output-basename 'humann2' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
26 --pathways 'metacyc'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
27
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
28 humann2 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
29 --input 'test-data/input_sequences.fasta' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
30 -o 'humann2_output' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
31 --annotation-gene-index 8 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
32 --metaphlan-options="-t rel_ab" \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
33 --nucleotide-database 'test-data/' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
34 --protein-database 'test-data/' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
35 --evalue '1' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
36 --search-mode 'uniref90' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
37 --prescreen-threshold '0.01' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
38 --identity-threshold '50' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
39 --translated-subject-coverage-threshold '50' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
40 --translated-query-coverage-threshold '50' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
41 --translated-alignment 'rapsearch' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
42 --xipe 'off' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
43 --minpath 'on' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
44 --pick-frames 'on' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
45 --gap-fill 'off' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
46 --output-format 'tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
47 --output-max-decimals '10' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
48 --output-basename 'humann2' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
49 --pathways 'unipathway'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
50
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
51 # humann2_associate
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
52 humann2_associate \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
53 --input 'test-data/hmp_pathabund.txt' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
54 --focal-metadatum 'STSite' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
55 --last-metadatum 'STSite' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
56 --focal-type 'categorical' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
57 --fdr '0.2' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
58 --output 'test-data/associate_output.txt'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
59
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
60 # humann2_barplot
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
61 humann2_barplot \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
62 --input 'test-data/hmp_pathabund.txt' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
63 --focal-feature ANAGLYCOLYSIS-PWY \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
64 --sort none \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
65 --last-metadatum STSite \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
66 --focal-metadatum STSite \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
67 --scaling none \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
68 --width 5 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
69 --dimensions 8 4 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
70 --output test-data/barplot1.png
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
71
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
72 humann2_barplot \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
73 --input 'test-data/hmp_pathabund.txt' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
74 --focal-feature ANAGLYCOLYSIS-PWY \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
75 --sort sum \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
76 --last-metadatum STSite \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
77 --focal-metadatum STSite \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
78 --scaling pseudolog \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
79 --width 5 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
80 --dimensions 8 4 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
81 --output test-data/barplot2.pdf
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
82
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
83 humann2_barplot \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
84 --input 'test-data/hmp_pathabund.txt' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
85 --focal-feature ANAGLYCOLYSIS-PWY \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
86 --sort metadata \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
87 --last-metadatum STSite \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
88 --focal-metadatum STSite \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
89 --exclude-unclassified \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
90 --scaling none \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
91 --as-genera \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
92 --grid \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
93 --remove-zeroes \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
94 --width 5 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
95 --dimensions 8 4 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
96 --output test-data/barplot3.svg
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
97
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
98 humann2_barplot \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
99 --input 'test-data/hmp_pathabund.txt' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
100 --focal-feature ANAGLYCOLYSIS-PWY \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
101 --top-strata 12 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
102 --sort sum \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
103 --last-metadatum STSite \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
104 --focal-metadatum STSite \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
105 --exclude-unclassified \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
106 --scaling normalize \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
107 --width 5 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
108 --dimensions 8 4 \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
109 --output test-data/barplot4.eps
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
110
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
111 # humann2_regroup_table
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
112 humann2_regroup_table \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
113 --input 'test-data/demo_genefamilies.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
114 -o 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
115 --function 'sum' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
116 --groups 'uniref90_infogo1000' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
117 --ungrouped 'Y' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
118 --protected 'Y'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
119
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
120 humann2_regroup_table \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
121 --input 'test-data/demo_genefamilies.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
122 -o 'test-data/regrouped_gene_families_to_ko.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
123 --function 'mean' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
124 --groups 'uniref90_ko' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
125 --ungrouped 'Y' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
126 --protected 'Y'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
127
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
128 humann2_regroup_table \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
129 --input 'test-data/demo_genefamilies.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
130 -o 'test-data/regrouped_gene_families_to_rxn.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
131 --function 'sum' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
132 --groups 'uniref90_rxn' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
133 --ungrouped 'Y' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
134 --protected 'Y'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
135
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
136 # humann2_renorm_table
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
137 humann2_renorm_table \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
138 --input 'test-data/demo_pathabundance.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
139 -o 'test-data/cpm_community_renormalized_pathway_abundance.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
140 --units 'cpm' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
141 --mode 'community' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
142 --special 'n'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
143
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
144 humann2_renorm_table \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
145 --input 'test-data/demo_pathabundance.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
146 -o 'test-data/relab_levelwise_renormalized_pathway_abundance.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
147 --units 'relab' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
148 --mode 'levelwise' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
149 --special 'y'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
150
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
151 # humann2_join_tables
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
152 mkdir join_table_tmp_dir
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
153 cp 'test-data/demo_pathabundance.tsv' join_table_tmp_dir
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
154 cp 'test-data/demo_pathcoverage.tsv' join_table_tmp_dir
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
155 humann2_join_tables \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
156 -i 'join_table_tmp_dir' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
157 -o 'test-data/joined_pathway_coverage_abundance.tsv'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
158
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
159 # humann2_merge_abundance_tables
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
160 humann2_merge_abundance_tables \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
161 --input-genes 'test-data/demo_genefamilies.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
162 --input-pathways 'test-data/demo_pathabundance.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
163 -o 'test-data/merged_gene_families_pathways_abundances.tsv'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
164
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
165 # humann2_reduce_table
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
166 humann2_reduce_table \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
167 --input 'test-data/demo_genefamilies.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
168 -o 'test-data/max_reduced_gene_family_abundance.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
169 --function 'max' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
170 --sort-by 'name'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
171
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
172 # humann2_rename_table
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
173 humann2_rename_table \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
174 --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
175 --names 'infogo1000' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
176 -o 'test-data/renamed_info1000.tsv'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
177
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
178 humann2_rename_table \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
179 --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
180 --custom 'test-data/rename_mapping' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
181 -o 'test-data/renamed_mapping_info1000.tsv'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
182
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
183 # humann2_rna_dna_norm
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
184 humann2_rna_dna_norm \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
185 --input_dna 'test-data/rna_dna_norm-dna.txt' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
186 --input_rna 'test-data/rna_dna_norm-rna.txt' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
187 --output_basename 'results1' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
188 --method 'laplace'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
189
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
190 humann2_rna_dna_norm \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
191 --input_dna 'test-data/rna_dna_norm-dna.txt' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
192 --input_rna 'test-data/rna_dna_norm-rna.txt' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
193 --output_basename 'results2' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
194 --method 'witten_bell' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
195 --log_transform \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
196 --log_base '2'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
197
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
198 # humann2_split_stratified_table
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
199 humann2_split_stratified_table \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
200 --input 'test-data/demo_genefamilies.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
201 --output 'split_stratified_table'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
202
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
203 # humann2_split_table
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
204 mkdir split_table_tmp_dir
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
205 humann2_split_table \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
206 --input 'test-data/joined_pathway_coverage_abundance.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
207 -o 'split_table_tmp_dir'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
208 cp 'split_table_tmp_dir/demo_Abundance.tsv' 'test-data/'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
209 cp 'split_table_tmp_dir/demo_Coverage.tsv' 'test-data/'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
210
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
211 # humann2_strain_profiler
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
212 humann2_strain_profiler \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
213 --input 'test-data/strain_profiler-input.txt' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
214 --critical_mean '1' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
215 --critical_count '2' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
216 --pinterval '1e-10' '1' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
217 --critical_samples '2'
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
218
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
219 # humann2_unpack_pathways
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
220 humann2_unpack_pathways \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
221 --input-genes 'test-data/demo_genefamilies.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
222 --input-pathways 'test-data/demo_pathabundance.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
223 --output unpack1
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
224
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
225 humann2_unpack_pathways \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
226 --input-genes 'test-data/demo_genefamilies.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
227 --input-pathways 'test-data/demo_pathabundance.tsv' \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
228 --remove-taxonomy \
d2e4fee96dd1 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents:
diff changeset
229 --output unpack2