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

Fixes
author florianbegusch
date Wed, 31 Jul 2019 03:06:00 -0400
parents 370e0b6e9826
children f190567fe3f6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="merge_feature_table_and_taxonomy" name="merge feature table and taxonomy" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description>- Merge features and taxonomy into a single biom file.</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 mkdir out;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
4
florianbegusch
parents: 0
diff changeset
10 qiime tools export --input-path $taxonomy_qza --output-path out;
florianbegusch
parents: 0
diff changeset
11 qiime tools export --input-path $biom_qza --output-path out;
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 sed -i '1s;^;#;' out/*.tsv;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 sed -i 's/Confidence/confidence/g' out/*.tsv;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 sed -i 's/Taxon/taxonomy/g' out/*.tsv;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 sed -i 's/Feature ID/OTU ID/g' out/*.tsv;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 biom add-metadata -i out/*.biom -o table_with_sample_metadata.biom --observation-metadata-fp out/*.tsv
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 mv *.biom $biom_and_tax_merged</command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 <param label="Feature table" name="biom_qza" type="data" format="qza,no_unzip.zip" collection_type="list"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 <param label="Taxonomy" name="taxonomy_qza" type="data" format="qza,no_unzip.zip"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 <data format="biom2" label="${tool.name} on ${on_string}: biom_and_tax_merged.biom" name="biom_and_tax_merged"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28 <help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 </help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 <expand macro="qiime_citation" />
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 </tool>