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comparison compleasm.xml @ 0:803d166831c8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 025282d56217bb501fcae8500546dec4ddf63949
author iuc
date Wed, 24 Jul 2024 17:43:01 +0000
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1 <tool id="compleasm" name="compleasm" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>completeness of genome assemblies</description>
3 <macros>
4 <import>macros.xml</import>
5 </macros>
6 <xrefs>
7 <xref type="bio.tools">compleasm</xref>
8 </xrefs>
9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">compleasm</requirement>
11 </requirements>
12 <version_command>compleasm --version</version_command>
13 <command><![CDATA[
14
15 mkdir -p galaxy_db &&
16 cp -r '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/' &&
17
18 compleasm run
19 -a '$input'
20 -o galaxy_output
21 --mode $mode
22 -L 'galaxy_db'
23 -l '$lineage_dataset'
24 -t "\${GALAXY_SLOTS:-1}"
25
26 #if str($specified_contigs) != '':
27 --specified_contigs '$specified_contigs'
28 #end if
29
30 ]]></command>
31 <inputs>
32 <param argument="-a" name="input" type="data" format="fasta" label="Input genome file"/>
33 <param name="mode" type="select" label="The mode of evaluation" help="If you want to use hmmsearch, select BUSCO mode. Otherwise, select lite mode">
34 <option value="busco" selected="true">BUSCO</option>
35 <option value="lite">Lite</option>
36 </param>
37
38 <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">
39 <sanitizer invalid_char="">
40 <valid initial="string.letters,string.digits">
41 <add value="_" />
42 </valid>
43 </sanitizer>
44 <validator type="regex">[0-9a-zA-Z_ ]+</validator>
45 </param>
46
47 <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
48 <option value="full_table_busco" selected="true">full busco table</option>
49 <option value="full_table">full table</option>
50 <option value="miniprot">miniprot</option>
51 <option value="translated_protein">translated proteins</option>
52 </param>
53
54 <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false">
55 <options from_data_table="busco_database"/>
56 </param>
57
58 <param name="lineage_dataset" type="select" label="Lineage">
59 <expand macro="lineages"/>
60 </param>
61 </inputs>
62
63 <outputs>
64 <data name='full_table_busco' format='tsv' label="${tool.name} on ${on_string}: full table BUSCO" from_work_dir="galaxy_output/*_odb10/full_table_busco_format.tsv">
65 <filter>outputs and 'full_table_busco' in outputs</filter>
66 </data>
67 <data name='full_table' format='tsv' label="${tool.name} on ${on_string}: full table" from_work_dir="galaxy_output/*_odb10/full_table.tsv">
68 <filter>outputs and 'full_table' in outputs</filter>
69 </data>
70 <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy_output/*_odb10/miniprot_output.gff">
71 <filter>outputs and 'miniprot' in outputs</filter>
72 </data>
73 <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta">
74 <filter>outputs and 'translated_protein' in outputs</filter>
75 </data>
76 </outputs>
77
78 <tests>
79 <test expect_num_outputs="4">
80 <param name="input" value="small_genome.fasta"/>
81 <param name="mode" value="busco"/>
82 <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/>
83 <param name="busco_database" value="eukaryota_odb10"/>
84 <param name="lineage_dataset" value="eukaryota_odb10"/>
85 <output name="full_table_busco">
86 <assert_contents>
87 <has_text text="Busco id"/>
88 <has_text text="Missing"/>
89 </assert_contents>
90 </output>
91 <output name="full_table">
92 <assert_contents>
93 <has_text text="Gene"/>
94 <has_text text="Missing"/>
95 </assert_contents>
96 </output>
97 <output name="miniprot">
98 <assert_contents>
99 <has_text text="##gff-version 3"/>
100 </assert_contents>
101 </output>
102 <output name="translated_protein">
103 <assert_contents>
104 <has_text text="GGWLIGNGGAGGSGAAGVNGGAGGNGGAGGNGGAGG"/>
105 <has_text text="AAVFADRGAHVVLAVRNLEKGNAARARIMAARPGAHVTLQQLDLCSLDSVRAAADALRTAYPRIDVLINNAGVMW"/>
106 </assert_contents>
107 </output>
108 </test>
109 </tests>
110 <help><![CDATA[
111
112 compleasm_ assesses genome completeness based on genome assembly.
113
114 .. _compleasm: https://github.com/huangnengCSU/compleasm
115
116 ]]>
117 </help>
118 <expand macro="citation"/>
119 </tool>