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05d.collapse-taxa.sh
44 lines (36 loc) · 1.21 KB
/
05d.collapse-taxa.sh
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#!/bin/bash
source ./util.sh
mkdir -p ${d}/taxa
if [[ ${TMI_DATATYPE} == 'WGS' ]];
then
qiime taxa collapse \
--i-table ${d}/$(tag_treeoverlap).biom.qza \
--i-taxonomy ${d}/$(tag_mindepth).taxonomy.qza \
--p-level 7 \
--o-collapsed-table ${d}/taxa/species.qza
fi
qiime taxa collapse \
--i-table ${d}/$(tag_treeoverlap).biom.qza \
--i-taxonomy ${d}/$(tag_mindepth).taxonomy.qza \
--p-level 6 \
--o-collapsed-table ${d}/taxa/genus.qza
qiime taxa collapse \
--i-table ${d}/$(tag_treeoverlap).biom.qza \
--i-taxonomy ${d}/$(tag_mindepth).taxonomy.qza \
--p-level 5 \
--o-collapsed-table ${d}/taxa/family.qza
qiime taxa collapse \
--i-table ${d}/$(tag_treeoverlap).biom.qza \
--i-taxonomy ${d}/$(tag_mindepth).taxonomy.qza \
--p-level 4 \
--o-collapsed-table ${d}/taxa/order.qza
qiime taxa collapse \
--i-table ${d}/$(tag_treeoverlap).biom.qza \
--i-taxonomy ${d}/$(tag_mindepth).taxonomy.qza \
--p-level 3 \
--o-collapsed-table ${d}/taxa/class.qza
qiime taxa collapse \
--i-table ${d}/$(tag_treeoverlap).biom.qza \
--i-taxonomy ${d}/$(tag_mindepth).taxonomy.qza \
--p-level 2 \
--o-collapsed-table ${d}/taxa/phylum.qza