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comparison compleasm.xml @ 5:7109a27a11db draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 0db08b58079fe83ce390bac19bcb056ed44932d3
author iuc
date Mon, 20 Jan 2025 09:55:04 +0000
parents 8f20a5b9b282
children
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4:8f20a5b9b282 5:7109a27a11db
9 <requirements> 9 <requirements>
10 <requirement type="package" version="@TOOL_VERSION@">compleasm</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">compleasm</requirement>
11 </requirements> 11 </requirements>
12 <version_command>compleasm --version</version_command> 12 <version_command>compleasm --version</version_command>
13 <command><![CDATA[ 13 <command><![CDATA[
14 14 mkdir -p 'galaxy_db/' &&
15 mkdir -p galaxy_db && 15 ln -s '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/${lineage_dataset}' &&
16 cp -r '${busco_database.fields.path}/lineages/${lineage_dataset}/' 'galaxy_db/' && 16 ## Create a compleasm-specific empty file to avoid redownloading the lineage data (https://github.com/huangnengCSU/compleasm/blob/0.2.6/compleasm.py#L165)
17 touch 'galaxy_db/${lineage_dataset}.done' &&
17 18
18 compleasm run 19 compleasm run
19 -a '$input' 20 -a '$input'
20 -o galaxy_output 21 -o galaxy_output
21 --mode $mode 22 --mode $mode
22 -L 'galaxy_db' 23 -L 'galaxy_db'
23 -l '$lineage_dataset' 24 -l '$lineage_dataset'
24 -t "\${GALAXY_SLOTS:-1}" 25 -t "\${GALAXY_SLOTS:-1}"
25 26
26 #if str($specified_contigs) != '': 27 #if str($specified_contigs) != '':
27 --specified_contigs '$specified_contigs' 28 --specified_contigs '$specified_contigs'
28 #end if 29 #end if
29 30
41 <add value="_" /> 42 <add value="_" />
42 </valid> 43 </valid>
43 </sanitizer> 44 </sanitizer>
44 <validator type="regex">[0-9a-zA-Z_ ]+</validator> 45 <validator type="regex">[0-9a-zA-Z_ ]+</validator>
45 </param> 46 </param>
46 47
47 <param name="outputs" type="select" multiple="true" label="Which outputs should be generated"> 48 <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
48 <option value="full_table_busco" selected="true">full busco table</option> 49 <option value="full_table_busco" selected="true">full busco table</option>
49 <option value="full_table">full table</option> 50 <option value="full_table">full table</option>
50 <option value="miniprot">miniprot</option> 51 <option value="miniprot">miniprot</option>
51 <option value="translated_protein">translated proteins</option> 52 <option value="translated_protein">translated proteins</option>
70 <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy_output/*_odb10/miniprot_output.gff"> 71 <data name='miniprot' format='gff3' label="${tool.name} on ${on_string}: Miniprot" from_work_dir="galaxy_output/*_odb10/miniprot_output.gff">
71 <filter>outputs and 'miniprot' in outputs</filter> 72 <filter>outputs and 'miniprot' in outputs</filter>
72 </data> 73 </data>
73 <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta"> 74 <data name='translated_protein' format='fasta' label="${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 <filter>outputs and 'translated_protein' in outputs</filter>
75 </data> 76 </data>
76 </outputs> 77 </outputs>
77 78
78 <tests> 79 <tests>
79 <test expect_num_outputs="4"> 80 <test expect_num_outputs="4">
80 <param name="input" value="small_genome.fasta"/> 81 <param name="input" value="small_genome.fasta"/>
81 <param name="mode" value="busco"/> 82 <param name="mode" value="busco"/>
82 <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/> 83 <param name="outputs" value="full_table_busco,full_table,miniprot,translated_protein"/>
83 <param name="busco_database" value="eukaryota_odb10"/> 84 <param name="busco_database" value="entomoplasmatales_odb10"/>
84 <param name="lineage_dataset" value="eukaryota_odb10"/> 85 <param name="lineage_dataset" value="entomoplasmatales_odb10"/>
85 <output name="full_table_busco"> 86 <output name="full_table_busco">
86 <assert_contents> 87 <assert_contents>
87 <has_text text="Busco id"/> 88 <has_text text="Busco id"/>
88 <has_text text="Missing"/> 89 <has_text text="496at186328&#009;Missing"/>
90 <has_text text="165at186328&#009;Complete"/>
91 <has_text text="421at186328&#009;Complete"/>
92 <has_text text="90at186328&#009;Complete"/>
89 </assert_contents> 93 </assert_contents>
90 </output> 94 </output>
91 <output name="full_table"> 95 <output name="full_table">
92 <assert_contents> 96 <assert_contents>
93 <has_text text="Gene"/> 97 <has_text text="Gene&#009;Status"/>
94 <has_text text="Missing"/> 98 <has_text text="496at186328&#009;Missing"/>
99 <has_text text="165at186328&#009;Single"/>
100 <has_text text="421at186328&#009;Single"/>
101 <has_text text="90at186328&#009;Single"/>
95 </assert_contents> 102 </assert_contents>
96 </output> 103 </output>
97 <output name="miniprot"> 104 <output name="miniprot">
98 <assert_contents> 105 <assert_contents>
99 <has_text text="##gff-version 3"/> 106 <has_text text="##gff-version 3"/>
100 </assert_contents> 107 </assert_contents>
101 </output> 108 </output>
102 <output name="translated_protein"> 109 <output name="translated_protein">
103 <assert_contents> 110 <assert_contents>
104 <has_text text="GGWLIGNGGAGGSGAAGVNGGAGGNGGAGGNGGAGG"/> 111 <has_text text="EKDFYQELGVSSDASPEEIKRAYRKLARDLHPDANPGNPAA"/>
105 <has_text text="AAVFADRGAHVVLAVRNLEKGNAARARIMAARPGAHVTLQQLDLCSLDSVRAAADALRTAYPRIDVLINNAGVMW"/> 112 <has_text text="AASITILEGLEAVRKRPGMYIGSTGERGLHHLIWEVVD"/>
106 </assert_contents> 113 </assert_contents>
107 </output> 114 </output>
115 <assert_stdout>
116 <has_text text="S:1.20%, 4"/>
117 </assert_stdout>
108 </test> 118 </test>
109 </tests> 119 </tests>
110 <help><![CDATA[ 120 <help><![CDATA[
111 121
112 compleasm_ assesses genome completeness based on genome assembly. 122 compleasm_ assesses genome completeness based on genome assembly.
113 123
114 .. _compleasm: https://github.com/huangnengCSU/compleasm 124 .. _compleasm: https://github.com/huangnengCSU/compleasm
115 125
116 ]]> 126 ]]>
117 </help> 127 </help>
118 <expand macro="citation"/> 128 <expand macro="citation"/>
119 </tool> 129 </tool>