Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/merge_feature_table_and_taxonomy.xml @ 4:914fa4daf16a draft
Fixes
author | florianbegusch |
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date | Wed, 31 Jul 2019 03:06:00 -0400 |
parents | 370e0b6e9826 |
children | f190567fe3f6 |
comparison
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3:558645416841 | 4:914fa4daf16a |
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5 <requirement type="package" version="2019.4">qiime2</requirement> | 5 <requirement type="package" version="2019.4">qiime2</requirement> |
6 </requirements> | 6 </requirements> |
7 <command> | 7 <command> |
8 mkdir out; | 8 mkdir out; |
9 | 9 |
10 qiime tools export --input-path --output-path out $taxonomy_qza; | 10 qiime tools export --input-path $taxonomy_qza --output-path out; |
11 qiime tools export --input-path --output-path out $biom_qza; | 11 qiime tools export --input-path $biom_qza --output-path out; |
12 | 12 |
13 sed -i '1s;^;#;' out/*.tsv; | 13 sed -i '1s;^;#;' out/*.tsv; |
14 sed -i 's/Confidence/confidence/g' out/*.tsv; | 14 sed -i 's/Confidence/confidence/g' out/*.tsv; |
15 sed -i 's/Taxon/taxonomy/g' out/*.tsv; | 15 sed -i 's/Taxon/taxonomy/g' out/*.tsv; |
16 sed -i 's/Feature ID/OTU ID/g' out/*.tsv; | 16 sed -i 's/Feature ID/OTU ID/g' out/*.tsv; |