Mercurial > repos > iuc > extract_metaphlan_database

comparison extract_metaphlan_database.xml @ 0:5b2f8b6a3609 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/metaphlan/ commit 1e543a44ceffd8e4c5537b9015606ab3b90a114c"
author iuc
date Mon, 19 Apr 2021 20:55:20 +0000
parents
children 5eccd3d336a3
comparison
equal deleted inserted replaced
-1:000000000000 0:5b2f8b6a3609
1 <tool id="extract_metaphlan_database" name="Extract the marker sequences and metadata" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
2 <description>from the MetaPhlAn 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 '$metadata'
20 ]]></command>
21 <inputs>
22 <param name="cached_db" label="Cached database with clade-specific marker genes" type="select">
23 <options from_data_table="metaphlan_database">
24 <validator message="No MetaPhlAn database is available" type="no_options" />
25 </options>
26 </param>
27 </inputs>
28 <outputs>
29 <data name="sequences" format="fasta" label="${tool.name} on ${on_string}: Marker seqeunces from MetaPhlAn database" />
30 <data name="metadata" format="json" label="${tool.name} on ${on_string}: Marker metadata from MetaPhlAn database" />
31 </outputs>
32 <tests>
33 <test expect_num_outputs="2">
34 <param name="cached_db" value="test-db-20210409"/>
35 <output name="sequences" file="test-db.fasta" ftype="fasta" compare="sim_size">
36 <assert_contents>
37 <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"/>
38 </assert_contents>
39 </output>
40 <output name="metadata" file="test-db.json" ftype="json" compare="sim_size">
41 <assert_contents>
42 <has_text text="13076__A0A2I1PE66__CYJ72_10760"/>
43 <has_text text="k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Aerococcaceae|g__Globicatella|s__Globicatella_sanguinis"/>
44 <has_text text="GCA_002847845"/>
45 <has_text text="clade"/>
46 <has_text text="ext"/>
47 <has_text text="len"/>
48 <has_text text="taxon"/>
49 <has_text text="markers"/>
50 <has_text text="taxonomy"/>
51 <has_text text="merged_taxon"/>
52 </assert_contents>
53 </output>
54 </test>
55 </tests>
56 <help><![CDATA[
57 What it does
58 ============
59
60 Reconstruct the marker sequences (in fasta format) and metadata (in JSON) from the MetaPhlAn BowTie2 database
61
62 Outputs
63 =======
64
65 - Fasta file with marker sequences.
66
67 This file can be used to add new marker sequences and then customizing the database.
68
69 - JSON file with marker metadata
70
71 ]]></help>
72 <expand macro="citations"/>
73 </tool>