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
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children 914fa4daf16a
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-1:000000000000 0:370e0b6e9826
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>