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comparison compleasm.xml @ 0:07a74537acd5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 89b9cc3af83916f8d14911ac3484ad2e35ded0a4
author iuc
date Wed, 14 Feb 2024 14:31:44 +0000
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children 79413aecc398
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1 <tool id="compleasm" name="compleasm" version="@TOOL_VERSION@+galaxy0" profile="20.01">
2 <description>completeness of genome assemblies</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">compleasm</requirement>
8 </requirements>
9 <command><![CDATA[
10 compleasm run
11 -a '$input'
12 -o galaxy
13 --mode $mode
14 -l '$busco_database'
15
16 #if str($specified_contigs) != '':
17 --specified_contigs '$specified_contigs'
18 #end if
19
20 ]]></command>
21 <inputs>
22 <param argument="-a" name="input" type="data" format="fasta" label="Input genome file"/>
23 <param name="mode" type="select" label="The mode of evaluation" help="If you want to use hmmsearch, select BUSCO mode. Otherwise, select lite mode">
24 <option value="busco" selected="true">BUSCO</option>
25 <option value="lite">Lite</option>
26 </param>
27
28 <param argument="--specified_contigs" type="text" label="Specify the contigs to be evaluated" optional="true" help="e.g. chr1 chr2 chr3. If not specified, all contigs will be evaluated">
29 <sanitizer invalid_char="">
30 <valid initial="string.letters,string.digits">
31 <add value="_" />
32 </valid>
33 </sanitizer>
34 <validator type="regex">[0-9a-zA-Z_ ]+</validator>
35 </param>
36
37 <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
38 <option value="full_table_busco" selected="true">full busco table</option>
39 <option value="full_table">full table</option>
40 <option value="miniprot">miniprot</option>
41 <option value="translated_protein">translated proteins</option>
42 </param>
43
44 <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false">
45 <options from_data_table="busco_database"/>
46 </param>
47 </inputs>
48
49 <outputs>
50 <data name='full_table_busco' format='tsv' label="${tool.name} on ${on_string}: full table BUSCO" from_work_dir="galaxy/*_odb10/full_table_busco_format.tsv">
51 <filter>outputs and 'full_table_busco' in outputs</filter>
52 </data>
53 <data name='full_table' format='tsv' label="${tool.name} on ${on_string}: full table" from_work_dir="galaxy/*_odb10/full_table.tsv">
54 <filter>outputs and 'full_table' in outputs</filter>
55 </data>
56 <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy/*_odb10/miniprot_output.gff">
57 <filter>outputs and 'miniprot' in outputs</filter>
58 </data>
59 <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy/*_odb10/translated_protein.fasta">
60 <filter>outputs and 'translated_protein' in outputs</filter>
61 </data>
62 </outputs>
63
64 <tests>
65 <test expect_num_outputs="4">
66 <param name="input" value="small_genome.fasta"/>
67 <param name="mode" value="busco"/>
68 <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/>
69 <param name="busco_database" value="eukaryota"/>
70 <output name="full_table_busco">
71 <assert_contents>
72 <has_text text="Busco id"/>
73 <has_text text="Missing"/>
74 </assert_contents>
75 </output>
76 <output name="full_table">
77 <assert_contents>
78 <has_text text="Gene"/>
79 <has_text text="Missing"/>
80 </assert_contents>
81 </output>
82 <output name="miniprot">
83 <assert_contents>
84 <has_text text="##gff-version 3"/>
85 </assert_contents>
86 </output>
87 <output name="translated_protein">
88 <assert_contents>
89 <has_text text="GGWLIGNGGAGGSGAAGVNGGAGGNGGAGGNGGAGG"/>
90 <has_text text="AAVFADRGAHVVLAVRNLEKGNAARARIMAARPGAHVTLQQLDLCSLDSVRAAADALRTAYPRIDVLINNAGVMW"/>
91 </assert_contents>
92 </output>
93 </test>
94 </tests>
95 <help><![CDATA[
96
97 compleasm_ assesses genome completeness based on genome assembly.
98
99 .. _compleasm: https://github.com/huangnengCSU/compleasm
100
101 ]]>
102 </help>
103 <expand macro="citation"/>
104 </tool>