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comparison virhunter.xml @ 2:206c8054d74a draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 58587e05f604590c70550e13fc51b7425e916ed4
author iuc
date Sat, 14 Jan 2023 21:08:13 +0000
parents 341bcf4d4fcd
children
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1:341bcf4d4fcd 2:206c8054d74a
16 --test_ds '${fasta_file}' 16 --test_ds '${fasta_file}'
17 --weights '${weights.fields.path}' 17 --weights '${weights.fields.path}'
18 --out_path '${predicted_fragments.extra_files_path}' 18 --out_path '${predicted_fragments.extra_files_path}'
19 --return_viral True 19 --return_viral True
20 --limit $limit 20 --limit $limit
21 && cp '${predicted_fragments.extra_files_path}'/predicted_fragments.csv predicted_fragments.csv 21 && cp '${predicted_fragments.extra_files_path}'/predicted_fragments.tsv predicted_fragments.tsv
22 && cp '${predicted_fragments.extra_files_path}'/predicted.csv predicted.csv 22 && cp '${predicted_fragments.extra_files_path}'/predicted.tsv predicted.tsv
23 && cp '${predicted_fragments.extra_files_path}'/viral.fasta viral.fasta 23 && cp '${predicted_fragments.extra_files_path}'/viral.fasta viral.fasta
24 24
25 ]]></command> 25 ]]></command>
26 <inputs> 26 <inputs>
27 <param name="fasta_file" type="data" format="fasta" label="DNA FASTA file"/> 27 <param name="fasta_file" type="data" format="fasta" label="DNA FASTA file"/>
31 </options> 31 </options>
32 </param> 32 </param>
33 <param argument="--limit" type="integer" min="0" value="750" label="Minimum contig length" help="Do not predict contigs shorter than this value. Default: 750" /> 33 <param argument="--limit" type="integer" min="0" value="750" label="Minimum contig length" help="Do not predict contigs shorter than this value. Default: 750" />
34 </inputs> 34 </inputs>
35 <outputs> 35 <outputs>
36 <data format="csv" name="predicted_fragments" from_work_dir="predicted_fragments.csv" label="${tool.name} on ${on_string}: predicted fragments"/> 36 <data format="tabular" name="predicted_fragments" from_work_dir="predicted_fragments.tsv" label="${tool.name} on ${on_string}: predicted fragments"/>
37 <data format="csv" name="predicted" from_work_dir="predicted.csv" label="${tool.name} on ${on_string}: predicted "/> 37 <data format="tabular" name="predicted" from_work_dir="predicted.tsv" label="${tool.name} on ${on_string}: predicted "/>
38 <data format="fasta" name="viral" from_work_dir="viral.fasta" label="${tool.name} on ${on_string}: viral FASTA file" /> 38 <data format="fasta" name="viral" from_work_dir="viral.fasta" label="${tool.name} on ${on_string}: viral FASTA file" />
39 </outputs> 39 </outputs>
40 <tests> 40 <tests>
41 <test> 41 <test>
42 <param name="fasta_file" value="viruses.fasta"/> 42 <param name="fasta_file" value="viruses.fasta"/>
43 <param name="weights" value="test"/> 43 <param name="weights" value="test"/>
44 <output name="predicted_fragments" file="predicted_fragments.csv" ftype="csv" lines_diff="2"/> 44 <output name="predicted_fragments" file="predicted_fragments.tsv" ftype="tabular" lines_diff="2"/>
45 <output name="predicted" file="predicted.csv" ftype="csv" lines_diff="2"/> 45 <output name="predicted" file="predicted.tsv" ftype="tabular" lines_diff="2"/>
46 <output name="viral" file="viral.fasta" ftype="fasta" lines_diff="2"/> 46 <output name="viral" file="viral.fasta" ftype="fasta" lines_diff="2"/>
47 </test> 47 </test>
48 </tests> 48 </tests>
49 49
50 <help> 50 <help>