Mercurial > repos > iuc > humann2_regroup_table

annotate generate_test_data @ 5:88ff1d78fd30 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/humann2 commit 55eb503f50c54695ec36c3d4671c2b3e64d05f40"
author iuc
date Fri, 05 Feb 2021 18:27:56 +0000
parents 1d141730ec69
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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diff changeset
1 #/usr/bin/env bash
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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2
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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3 # humann2
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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4 humann2 \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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5 --input 'test-data/input_sequences.fasta' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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6 -o 'humann2_output' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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7 --annotation-gene-index 8 \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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8 --taxonomic-profile 'test-data/taxonomic_profile.tabular' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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9 --metaphlan-options="-t rel_ab" \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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10 --nucleotide-database 'test-data/' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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11 --protein-database 'test-data/' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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12 --evalue '1' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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13 --search-mode 'uniref50' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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14 --prescreen-threshold '0.01' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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15 --identity-threshold '50' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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16 --translated-subject-coverage-threshold '50' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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17 --translated-query-coverage-threshold '50' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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18 --translated-alignment 'diamond' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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19 --xipe 'off' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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20 --minpath 'on' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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21 --pick-frames 'on' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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22 --gap-fill 'off' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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23 --output-format 'tsv' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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24 --output-max-decimals '10' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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25 --output-basename 'humann2' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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26 --pathways 'metacyc'
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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27
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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28 humann2 \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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29 --input 'test-data/input_sequences.fasta' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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30 -o 'humann2_output' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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31 --annotation-gene-index 8 \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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32 --metaphlan-options="-t rel_ab" \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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33 --nucleotide-database 'test-data/' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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34 --protein-database 'test-data/' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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35 --evalue '1' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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36 --search-mode 'uniref90' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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37 --prescreen-threshold '0.01' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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38 --identity-threshold '50' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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39 --translated-subject-coverage-threshold '50' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
parents:
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40 --translated-query-coverage-threshold '50' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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41 --translated-alignment 'rapsearch' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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42 --xipe 'off' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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43 --minpath 'on' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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44 --pick-frames 'on' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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45 --gap-fill 'off' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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46 --output-format 'tsv' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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47 --output-max-decimals '10' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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48 --output-basename 'humann2' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
iuc
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49 --pathways 'unipathway'
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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50
1
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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51 # humann2_associate
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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52 humann2_associate \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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53 --input 'test-data/hmp_pathabund.txt' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents: 0
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54 --focal-metadatum 'STSite' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents: 0
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55 --last-metadatum 'STSite' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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56 --focal-type 'categorical' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents: 0
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57 --fdr '0.2' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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58 --output 'test-data/associate_output.txt'
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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59
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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60 # humann2_barplot
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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61 humann2_barplot \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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62 --input 'test-data/hmp_pathabund.txt' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents: 0
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63 --focal-feature ANAGLYCOLYSIS-PWY \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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64 --sort none \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents: 0
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65 --last-metadatum STSite \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents: 0
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66 --focal-metadatum STSite \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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67 --scaling none \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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68 --width 5 \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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69 --dimensions 8 4 \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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70 --output test-data/barplot1.png
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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71
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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72 humann2_barplot \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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73 --input 'test-data/hmp_pathabund.txt' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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74 --focal-feature ANAGLYCOLYSIS-PWY \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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75 --sort sum \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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76 --last-metadatum STSite \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents: 0
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77 --focal-metadatum STSite \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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78 --scaling pseudolog \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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79 --width 5 \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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80 --dimensions 8 4 \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
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81 --output test-data/barplot2.pdf
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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82
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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83 humann2_barplot \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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84 --input 'test-data/hmp_pathabund.txt' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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85 --focal-feature ANAGLYCOLYSIS-PWY \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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86 --sort metadata \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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87 --last-metadatum STSite \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
iuc
parents: 0
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88 --focal-metadatum STSite \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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89 --exclude-unclassified \
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90 --scaling none \
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91 --as-genera \
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92 --grid \
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93 --remove-zeroes \
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94 --width 5 \
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95 --dimensions 8 4 \
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96 --output test-data/barplot3.svg
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97
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98 humann2_barplot \
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99 --input 'test-data/hmp_pathabund.txt' \
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100 --focal-feature ANAGLYCOLYSIS-PWY \
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101 --top-strata 12 \
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102 --sort sum \
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103 --last-metadatum STSite \
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104 --focal-metadatum STSite \
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105 --exclude-unclassified \
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106 --scaling normalize \
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107 --width 5 \
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108 --dimensions 8 4 \
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109 --output test-data/barplot4.eps
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110
0
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111 # humann2_regroup_table
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112 humann2_regroup_table \
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113 --input 'test-data/demo_genefamilies.tsv' \
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114 -o 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
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115 --function 'sum' \
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116 --groups 'uniref90_infogo1000' \
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117 --ungrouped 'Y' \
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118 --protected 'Y'
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119
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120 humann2_regroup_table \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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121 --input 'test-data/demo_genefamilies.tsv' \
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122 -o 'test-data/regrouped_gene_families_to_ko.tsv' \
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123 --function 'mean' \
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124 --groups 'uniref90_ko' \
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125 --ungrouped 'Y' \
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126 --protected 'Y'
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127
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128 humann2_regroup_table \
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129 --input 'test-data/demo_genefamilies.tsv' \
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130 -o 'test-data/regrouped_gene_families_to_rxn.tsv' \
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131 --function 'sum' \
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132 --groups 'uniref90_rxn' \
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133 --ungrouped 'Y' \
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134 --protected 'Y'
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135
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136 # humann2_renorm_table
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137 humann2_renorm_table \
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138 --input 'test-data/demo_pathabundance.tsv' \
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139 -o 'test-data/cpm_community_renormalized_pathway_abundance.tsv' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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140 --units 'cpm' \
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141 --mode 'community' \
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142 --special 'n'
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143
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144 humann2_renorm_table \
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145 --input 'test-data/demo_pathabundance.tsv' \
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146 -o 'test-data/relab_levelwise_renormalized_pathway_abundance.tsv' \
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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147 --units 'relab' \
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148 --mode 'levelwise' \
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149 --special 'y'
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150
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151 # humann2_join_tables
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152 mkdir join_table_tmp_dir
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153 cp 'test-data/demo_pathabundance.tsv' join_table_tmp_dir
a1747df2bc21 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit b46aa969c01b7e5f4f133192899fa4da286ecf89-dirty
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154 cp 'test-data/demo_pathcoverage.tsv' join_table_tmp_dir
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155 humann2_join_tables \
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156 -i 'join_table_tmp_dir' \
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157 -o 'test-data/joined_pathway_coverage_abundance.tsv'
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158
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159 # humann2_merge_abundance_tables
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160 humann2_merge_abundance_tables \
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161 --input-genes 'test-data/demo_genefamilies.tsv' \
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162 --input-pathways 'test-data/demo_pathabundance.tsv' \
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163 -o 'test-data/merged_gene_families_pathways_abundances.tsv'
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164
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165 # humann2_reduce_table
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166 humann2_reduce_table \
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167 --input 'test-data/demo_genefamilies.tsv' \
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168 -o 'test-data/max_reduced_gene_family_abundance.tsv' \
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169 --function 'max' \
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170 --sort-by 'name'
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171
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172 # humann2_rename_table
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173 humann2_rename_table \
1
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174 --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
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175 --names 'infogo1000' \
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176 -o 'test-data/renamed_info1000.tsv'
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177
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178 humann2_rename_table \
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179 --input 'test-data/regrouped_gene_families_to_infogo1000.tsv' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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180 --custom 'test-data/rename_mapping' \
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181 -o 'test-data/renamed_mapping_info1000.tsv'
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182
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183 # humann2_rna_dna_norm
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184 humann2_rna_dna_norm \
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185 --input_dna 'test-data/rna_dna_norm-dna.txt' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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186 --input_rna 'test-data/rna_dna_norm-rna.txt' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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187 --output_basename 'results1' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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188 --method 'laplace'
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189
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190 humann2_rna_dna_norm \
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191 --input_dna 'test-data/rna_dna_norm-dna.txt' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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192 --input_rna 'test-data/rna_dna_norm-rna.txt' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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193 --output_basename 'results2' \
1d141730ec69 planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee
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194 --method 'witten_bell' \
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195 --log_transform \
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196 --log_base '2'
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197
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198 # humann2_split_stratified_table
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199 humann2_split_stratified_table \
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200 --input 'test-data/demo_genefamilies.tsv' \
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201 --output 'split_stratified_table'
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202
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203 # humann2_split_table
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204 mkdir split_table_tmp_dir
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205 humann2_split_table \
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206 --input 'test-data/joined_pathway_coverage_abundance.tsv' \
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207 -o 'split_table_tmp_dir'
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208 cp 'split_table_tmp_dir/demo_Abundance.tsv' 'test-data/'
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209 cp 'split_table_tmp_dir/demo_Coverage.tsv' 'test-data/'
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210
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211 # humann2_strain_profiler
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212 humann2_strain_profiler \
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213 --input 'test-data/strain_profiler-input.txt' \
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214 --critical_mean '1' \
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215 --critical_count '2' \
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216 --pinterval '1e-10' '1' \
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217 --critical_samples '2'
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218
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219 # humann2_unpack_pathways
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220 humann2_unpack_pathways \
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221 --input-genes 'test-data/demo_genefamilies.tsv' \
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222 --input-pathways 'test-data/demo_pathabundance.tsv' \
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223 --output unpack1
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224
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225 humann2_unpack_pathways \
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226 --input-genes 'test-data/demo_genefamilies.tsv' \
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227 --input-pathways 'test-data/demo_pathabundance.tsv' \
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228 --remove-taxonomy \
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229 --output unpack2