Mercurial > repos > florianbegusch > qiime2_suite

comparison qiime2/merge_feature_table_and_taxonomy.xml @ 4:914fa4daf16a draft

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Fixes
author florianbegusch
date Wed, 31 Jul 2019 03:06:00 -0400
parents 370e0b6e9826
children f190567fe3f6
comparison
equal deleted inserted replaced
3:558645416841 4:914fa4daf16a
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;