Mercurial > repos > thanhlv > extract_metaphlan_database

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planemo upload for repository https://github.com/quadram-institute-bioscience/galaxy-tools/tree/master/tools/metaphlan/
author thanhlv
date Mon, 13 Feb 2023 11:37:08 +0000
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1 <tool id="extract_metaphlan_database" name="Extract the marker sequences and metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
2 <description>from the MetaPhlAn4 database</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <expand macro="edam_ontology"/>
7 <expand macro="requirements"/>
8 <version_command>metaphlan -v</version_command>
9 <command detect_errors="aggressive"><![CDATA[
10 bowtie2-inspect
11 '${cached_db.fields.path}/${cached_db.fields.dbkey}'
12 > '$sequences'
13
14 &&
15
16 python '$__tool_directory__/customizemetadata.py'
17 transform_pkl_to_json
18 --pkl '${cached_db.fields.path}/${cached_db.fields.dbkey}.pkl'
19 --json '$metadata'
20 ]]></command>
21 <inputs>
22 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
23 <options from_data_table="@IDX_DATA_TABLE@">
24 <filter type="static_value" column="4" value="@IDX_VERSION@"/>
25 <validator message="No MetaPhlAn database is available" type="no_options"/>
26 </options>
27 </param>
28 </inputs>
29 <outputs>
30 <data name="sequences" format="fasta" label="${tool.name} on ${on_string}: Marker seqeunces from MetaPhlAn database"/>
31 <data name="metadata" format="json" label="${tool.name} on ${on_string}: Marker metadata from MetaPhlAn database"/>
32 </outputs>
33 <tests>
34 <test expect_num_outputs="2">
35 <param name="cached_db" value="test-db-20210409"/>
36 <output name="sequences" file="test-db.fasta" ftype="fasta" compare="sim_size">
37 <assert_contents>
38 <has_line line=">13076__A0A2I1PE66__CYJ72_10760 UniRef90_A0A2I1PE66;k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis;GCA_002847845"/>
39 </assert_contents>
40 </output>
41 <output name="metadata" file="test-db.json" ftype="json" compare="sim_size">
42 <assert_contents>
43 <has_text text="13076__A0A2I1PE66__CYJ72_10760"/>
44 <has_text text="k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis"/>
45 <has_text text="GCA_002847845"/>
46 <has_text text="clade"/>
47 <has_text text="ext"/>
48 <has_text text="len"/>
49 <has_text text="taxon"/>
50 <has_text text="markers"/>
51 <has_text text="taxonomy"/>
52 <has_text text="merged_taxon"/>
53 </assert_contents>
54 </output>
55 </test>
56 </tests>
57 <help><![CDATA[
58 What it does
59 ============
60
61 Reconstruct the marker sequences (in fasta format) and metadata (in JSON) from the MetaPhlAn BowTie2 database
62
63 Outputs
64 =======
65
66 - Fasta file with marker sequences.
67
68 This file can be used to add new marker sequences and then customizing the database.
69
70 - JSON file with marker metadata
71
72 ]]></help>
73 <expand macro="citations"/>
74 </tool>