Mercurial > repos > thanhlv > extract_metaphlan_database

annotate generate_test_data.sh @ 0:ae891c1cbd27 draft default tip

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
author thanhlv
date Mon, 13 Feb 2023 11:37:08 +0000
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ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
thanhlv
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1 #/usr/bin/env bash
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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2
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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3 metaphlan_hclust_heatmap.py \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
thanhlv
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4 --in test-data/merged_community_profile.tabular \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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5 --out test-data/heatmap.png \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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6 -m 'average' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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7 -d 'braycurtis' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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8 -f 'correlation' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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9 --minv '0' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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10 --tax_lev 'a' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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11 --sdend_h '0.1' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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12 --fdend_w '0.1' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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13 --cm_h '0.03' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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14 --font_size '7' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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15 --clust_line_w '1' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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16 --perc '90' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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17 -c 'jet'
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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18
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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19 metaphlan_hclust_heatmap.py \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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20 --in test-data/merged_community_profile.tabular \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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21 --out test-data/heatmap.pdf \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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22 -m 'ward' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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23 -d 'euclidean' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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24 -f 'euclidean' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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25 --minv '0' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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26 --tax_lev 'a' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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27 --sdend_h '0.1' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
thanhlv
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28 --fdend_w '0.1' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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29 --cm_h '0.03' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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30 --font_size '7' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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31 --clust_line_w '1' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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32 --perc '90' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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33 -c 'pink'
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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34
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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35 metaphlan_hclust_heatmap.py \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
thanhlv
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36 --in test-data/merged_community_profile.tabular \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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37 --out test-data/heatmap.svg \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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38 -m 'complete' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
thanhlv
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39 -d 'hamming' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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40 -f 'matching' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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41 --minv '0' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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42 --tax_lev 'a' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
thanhlv
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43 --sdend_h '0.1' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
thanhlv
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44 --fdend_w '0.1' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
thanhlv
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45 --cm_h '0.03' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
thanhlv
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46 --font_size '7' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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47 --clust_line_w '1' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
thanhlv
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48 --perc '90' \
ae891c1cbd27 planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
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49 -c 'pink'