Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/merge_feature_table_and_taxonomy.xml @ 0:370e0b6e9826 draft
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| author | florianbegusch |
|---|---|
| date | Wed, 17 Jul 2019 03:05:17 -0400 |
| parents | |
| children | 914fa4daf16a |
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| -1:000000000000 | 0:370e0b6e9826 |
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| 1 <?xml version="1.0" ?> | |
| 2 <tool id="merge_feature_table_and_taxonomy" name="merge feature table and taxonomy" version="2019.4"> | |
| 3 <description>- Merge features and taxonomy into a single biom file.</description> | |
| 4 <requirements> | |
| 5 <requirement type="package" version="2019.4">qiime2</requirement> | |
| 6 </requirements> | |
| 7 <command> | |
| 8 mkdir out; | |
| 9 | |
| 10 qiime tools export --input-path --output-path out $taxonomy_qza; | |
| 11 qiime tools export --input-path --output-path out $biom_qza; | |
| 12 | |
| 13 sed -i '1s;^;#;' out/*.tsv; | |
| 14 sed -i 's/Confidence/confidence/g' out/*.tsv; | |
| 15 sed -i 's/Taxon/taxonomy/g' out/*.tsv; | |
| 16 sed -i 's/Feature ID/OTU ID/g' out/*.tsv; | |
| 17 | |
| 18 biom add-metadata -i out/*.biom -o table_with_sample_metadata.biom --observation-metadata-fp out/*.tsv | |
| 19 ; | |
| 20 mv *.biom $biom_and_tax_merged</command> | |
| 21 <inputs> | |
| 22 <param label="Feature table" name="biom_qza" type="data" format="qza,no_unzip.zip" collection_type="list"/> | |
| 23 <param label="Taxonomy" name="taxonomy_qza" type="data" format="qza,no_unzip.zip"/> | |
| 24 </inputs> | |
| 25 <outputs> | |
| 26 <data format="biom2" label="${tool.name} on ${on_string}: biom_and_tax_merged.biom" name="biom_and_tax_merged"/> | |
| 27 </outputs> | |
| 28 <help> | |
| 29 </help> | |
| 30 <macros> | |
| 31 <import>qiime_citation.xml</import> | |
| 32 </macros> | |
| 33 <expand macro="qiime_citation" /> | |
| 34 </tool> |