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comparison compleasm.xml @ 2:95716c25b2ab draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/compleasm/ commit 9c5d5e6f1813e5c0fd496a828a1fb5e3120f188c
author iuc
date Thu, 25 Sep 2025 11:37:36 +0000
parents a5671f66f255
children
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1:a5671f66f255 2:95716c25b2ab
33 <param argument="-a" name="input" type="data" format="fasta" label="Input genome file"/> 33 <param argument="-a" name="input" type="data" format="fasta" label="Input genome file"/>
34 <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 <param name="mode" type="select" label="The mode of evaluation" help="If you want to use hmmsearch, select BUSCO mode. Otherwise, select lite mode">
35 <option value="busco" selected="true">BUSCO</option> 35 <option value="busco" selected="true">BUSCO</option>
36 <option value="lite">Lite</option> 36 <option value="lite">Lite</option>
37 </param> 37 </param>
38
39 <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"> 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">
40 <sanitizer invalid_char=""> 39 <sanitizer invalid_char="">
41 <valid initial="string.letters,string.digits"> 40 <valid initial="string.letters,string.digits">
42 <add value="_" /> 41 <add value="_" />
43 </valid> 42 </valid>
48 <param name="outputs" type="select" multiple="true" label="Which outputs should be generated"> 47 <param name="outputs" type="select" multiple="true" label="Which outputs should be generated">
49 <option value="full_table_busco" selected="true">full busco table</option> 48 <option value="full_table_busco" selected="true">full busco table</option>
50 <option value="full_table">full table</option> 49 <option value="full_table">full table</option>
51 <option value="miniprot">miniprot</option> 50 <option value="miniprot">miniprot</option>
52 <option value="translated_protein">translated proteins</option> 51 <option value="translated_protein">translated proteins</option>
52 <option value="summary">summary</option>
53 </param> 53 </param>
54 54
55 <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false"> 55 <param name="busco_database" label="Choose the BUSCO database to be used" type="select" multiple="false">
56 <options from_data_table="busco_database"/> 56 <options from_data_table="busco_database"/>
57 </param> 57 </param>
71 <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 ${on_string}: Miniprot" from_work_dir="galaxy_output/*_odb10/miniprot_output.gff">
72 <filter>outputs and 'miniprot' in outputs</filter> 72 <filter>outputs and 'miniprot' in outputs</filter>
73 </data> 73 </data>
74 <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta"> 74 <data name='translated_protein' format='fasta' label="${tool.name} on ${on_string}: Translated protein" from_work_dir="galaxy_output/*_odb10/translated_protein.fasta">
75 <filter>outputs and 'translated_protein' in outputs</filter> 75 <filter>outputs and 'translated_protein' in outputs</filter>
76 </data>
77 <data name='summary' format='txt' label="${tool.name} on ${on_string}: Summary" from_work_dir="galaxy_output/summary.txt">
78 <filter>outputs and 'summary' in outputs</filter>
76 </data> 79 </data>
77 </outputs> 80 </outputs>
78 81
79 <tests> 82 <tests>
80 <test expect_num_outputs="4"> 83 <test expect_num_outputs="4">
114 </output> 117 </output>
115 <assert_stdout> 118 <assert_stdout>
116 <has_text text="S:1.20%, 4"/> 119 <has_text text="S:1.20%, 4"/>
117 </assert_stdout> 120 </assert_stdout>
118 </test> 121 </test>
122 <test expect_num_outputs="1">
123 <param name="input" value="small_genome.fasta"/>
124 <param name="mode" value="lite"/>
125 <param name="outputs" value="summary"/>
126 <param name="busco_database" value="entomoplasmatales_odb10"/>
127 <param name="lineage_dataset" value="entomoplasmatales_odb10"/>
128 <output name="summary">
129 <assert_contents>
130 <has_text text="## lineage: entomoplasmatales_odb10"/>
131 <has_text text="M:96.08%, 319"/>
132 <has_text text="N:332"/>
133 </assert_contents>
134 </output>
135 <assert_stdout>
136 <has_text text="S:3.01%, 10"/>
137 </assert_stdout>
138 </test>
119 </tests> 139 </tests>
120 <help><![CDATA[ 140 <help><![CDATA[
121 141
122 compleasm_ assesses genome completeness based on genome assembly. 142 compleasm_ assesses genome completeness based on genome assembly.
123 143