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