Mercurial > repos > iuc > deepvariant
annotate deepvariant.xml @ 6:1ad55977a040 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
| author | iuc |
|---|---|
| date | Thu, 12 Feb 2026 08:51:49 +0000 |
| parents | fd52f65372c9 |
| children |
| rev | line source |
|---|---|
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
1 <tool id='deepvariant' name='DeepVariant' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='@PROFILE@'> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
2 <description>deep learning-based variant caller</description> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
3 <macros> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
4 <import>macros.xml</import> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
5 </macros> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
6 <expand macro='edam_ontology' /> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
7 <expand macro='requirements' /> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
8 <command detect_errors='exit_code'><![CDATA[ |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
9 ln -s '${reads}' 'reads_alignment.$reads.ext' |
|
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
10 #if $reads.is_of_type("bam") |
|
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
11 && ln -s '${reads.metadata.bam_index}' reads_alignment.bam.bai |
|
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
12 #elif $reads.is_of_type("cram") |
|
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
13 && ln -s '${reads.metadata.cram_index}' reads_alignment.cram.crai |
|
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
14 #end if |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
15 #if $regions_conditional.regions_option == 'bed' |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
16 && ln -s '${regions_conditional.bed_file}' region.bed |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
17 #end if |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
18 #if $par_regions_bed |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
19 && ln -s '${par_regions_bed}' par_regions.bed |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
20 #end if |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
21 #set $logging_dir_value = None |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
22 #if $create_runtime_report |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
23 #set $logging_dir_value = 'logging' |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
24 && mkdir -p '$logging_dir_value' |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
25 #end if |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
26 #if $reference_genome.source == 'history': |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
27 #set $ref_genome = 'reference.fasta' |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
28 && ln -s -f '${reference_genome.history_item}' $ref_genome |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
29 && samtools faidx $ref_genome |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
30 #else: |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
31 #set $ref_genome = $reference_genome.index.fields.path |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
32 #end if |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
33 && run_deepvariant |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
34 --model_type=$model_type |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
35 --ref=$ref_genome |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
36 --reads='reads_alignment.$reads.ext' |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
37 #if $sample_name |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
38 --sample_name '$sample_name' |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
39 #end if |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
40 --output_vcf='./output.vcf.gz' |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
41 #if $output_gvcf |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
42 --output_gvcf='./output.g.vcf.gz' |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
43 #end if |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
44 #if $regions_conditional.regions_option == 'region' |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
45 --regions '$regions_conditional.region_literal' |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
46 #else if $regions_conditional.regions_option == 'bed' |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
47 --regions 'region.bed' |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
48 #end if |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
49 --disable_small_model=$disable_small_model |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
50 #if $haploid_contigs |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
51 --haploid_contigs='$haploid_contigs' |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
52 #end if |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
53 #if $par_regions_bed |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
54 --par_regions_bed='par_regions.bed' |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
55 #end if |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
56 #if $logging_dir_value |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
57 --logging_dir='$logging_dir_value' |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
58 #end if |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
59 #if $report_title |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
60 --report_title='$report_title' |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
61 #end if |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
62 --runtime_report=$create_runtime_report |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
63 #if $make_examples_extra_args |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
64 --make_examples_extra_args='$make_examples_extra_args' |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
65 #end if |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
66 #if $call_variants_extra_args |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
67 --call_variants_extra_args='$call_variants_extra_args' |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
68 #end if |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
69 #if $postprocess_variants_extra_args |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
70 --postprocess_variants_extra_args='$postprocess_variants_extra_args' |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
71 #end if |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
72 $vcf_stats_report |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
73 --num_shards=\${GALAXY_SLOTS:-2} |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
74 && gunzip './output.vcf.gz' |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
75 #if $output_gvcf |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
76 && gunzip './output.g.vcf.gz' |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
77 #end if |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
78 ]]> </command> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
79 <inputs> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
80 <conditional name="reference_genome"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
81 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options."> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
82 <option value="indexed" selected="true">Use a built-in genome</option> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
83 <option value="history">Use a genome from history</option> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
84 </param> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
85 <when value="indexed"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
86 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team."> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
87 <options from_data_table="fasta_indexes"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
88 <filter type="sort_by" column="2" /> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
89 <validator type="no_options" message="No genomes are available for the selected input dataset" /> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
90 </options> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
91 </param> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
92 </when> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
93 <when value="history"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
94 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" /> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
95 </when> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
96 </conditional> |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
97 <param argument="--reads" type="data" format="bam,cram" label="BAM file" help="An aligned reads file in BAM format. The reads must be aligned to the reference genome" /> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
98 <param argument="--sample_name" type="text" optional="true" label="Sample name" help="Sample name to use instead of the SM tag in the BAM header. Example: NA12878" /> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
99 <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
100 <option value="WGS">WGS: Illumina whole genome sequencing</option> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
101 <option value="WES">WES: Illumina whole exome sequencing</option> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
102 <option value="PACBIO">PacBio HiFi</option> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
103 <option value="HYBRID_PACBIO_ILLUMINA">Hybrid PacBio HiFi-Illumina</option> |
|
3
918c8b94c8d8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents:
2
diff
changeset
|
104 <option value="ONT_R104">ONT R10.4 simplex and duplex data</option> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
105 </param> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
106 <conditional name="regions_conditional"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
107 <param name="regions_option" type="select" label="Select specific regions to process" help="Restrict the analysis to specific regions. A space-separated list of chromosome regions to process. Individual elements can be region literals, such as chr20:10-20 or paths to BED files."> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
108 <option value="disabled" selected="True">Disabled</option> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
109 <option value="region">Specify region literals</option> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
110 <option value="bed">Provide a BED file</option> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
111 </param> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
112 <when value="disabled"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
113 <when value="region"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
114 <param name="region_literal" argument="--regions" type="text" label="Regions" help="This option refers to contigs present in the reference genome. These arguments accept space-separated lists, so all of the follow examples are valid arguments: 'chr20:10,000,000-11,000,000', 'chr20 chr21' and 'chr20'"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
115 <sanitizer invalid_char=""> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
116 <valid initial="string.letters,string.digits"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
117 <add value="," /> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
118 <add value=":" /> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
119 <add value="-" /> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
120 </valid> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
121 </sanitizer> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
122 <validator type="regex">[0-9a-zA-Z,:-]+</validator> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
123 </param> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
124 </when> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
125 <when value="bed"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
126 <param name="bed_file" argument="--regions" type="data" format="bed" label="BED file" help="The BED should the store genomic regions of interest" /> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
127 </when> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
128 </conditional> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
129 <param argument="--output_gvcf" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Generate genomic VCF (gVCF) output" help="The key difference between a regular VCF and a gVCF is that the gVCF has records for all sites, whether there is a variant call there or not. The goal is to have every site represented in the file in order to do joint analysis of a cohort in subsequent steps" /> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
130 <section name="advanced_options" title="Advanced options" expanded="false"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
131 <param argument="--disable_small_model" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Disable small model" help="Disable the use of the small model to call variants during make_examples." /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
132 <param argument="--haploid_contigs" type="text" optional="true" label="Haploid contigs" help="Comma-separated list of non-autosomal chromosomes. Example: chrX,chrY" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
133 <param argument="--par_regions_bed" type="data" format="bed" optional="true" label="PAR regions BED file" help="BED file of pseudoautosomal regions." /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
134 <param argument="--report_title" type="text" optional="true" label="Report title" help="Title for the VCF stats report (HTML). Example: NA12878 DeepVariant report" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
135 <param argument="--vcf_stats_report" type="boolean" truevalue="--vcf_stats_report=True" falsevalue="--vcf_stats_report=False" checked="False" label="Create VCF stats report (HTML)" help="Output a visual report (HTML) of statistics about the output VCF." /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
136 <param name="create_runtime_report" argument="--runtime_report" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Create runtime report" help="Output make_examples runtime metrics and create a visual runtime report." /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
137 </section> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
138 <section name="expert_options" title="Expert options (may increase runtime and disk usage)" expanded="false"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
139 <param argument="--make_examples_extra_args" type="text" optional="true" label="make_examples extra args" help="Comma-separated flag_name=flag_value for make_examples.py. Example: min_base_quality=10,min_mapping_quality=5" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
140 <param argument="--call_variants_extra_args" type="text" optional="true" label="call_variants extra args" help="Comma-separated flag_name=flag_value for call_variants.py. Example: allow_empty_examples=true,batch_size=1024" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
141 <param argument="--postprocess_variants_extra_args" type="text" optional="true" label="postprocess_variants extra args" help="Comma-separated flag_name=flag_value for postprocess_variants.py. Example: cnn_homref_call_min_gq=20.0" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
142 </section> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
143 </inputs> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
144 <outputs> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
145 <data name="vcf_file" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: VCF file"/> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
146 <data name="html_report" format="html" from_work_dir="output.visual_report.html" label="${tool.name} on ${on_string}: HTML report"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
147 <filter>advanced_options['vcf_stats_report']</filter> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
148 </data> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
149 <data name="runtime_report" format="html" from_work_dir="logging/make_examples_runtime_by_region_report.html" label="${tool.name} on ${on_string}: runtime report"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
150 <filter>advanced_options['create_runtime_report']</filter> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
151 </data> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
152 <data name="gvcf_file" format="vcf" from_work_dir="output.g.vcf" label="${tool.name} on ${on_string}: gVCF file"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
153 <filter>output_gvcf</filter> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
154 </data> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
155 </outputs> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
156 <tests> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
157 <test expect_num_outputs="2"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
158 <conditional name="reference_genome"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
159 <param name="source" value="history"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
160 <param name="history_item" value="reference.fasta"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
161 </conditional> |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
162 <param name="reads" value="reads.bam" ftype="bam"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
163 <param name="model_type" value="WGS"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
164 <param name="output_gvcf" value="False"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
165 <conditional name="regions_conditional"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
166 <param name="regions_option" value="disabled"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
167 </conditional> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
168 <section name="advanced_options"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
169 <param name="vcf_stats_report" value="True"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
170 <param name="report_title" value="Test Report Title"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
171 </section> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
172 <output name="vcf_file" ftype="vcf"> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
173 <assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
174 <has_text text="##fileformat=VCFv4.2"/> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
175 <has_text text="#CHROM"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
176 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
177 </output> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
178 <output name="html_report" ftype="html"> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
179 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
180 <is_valid_xml /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
181 <has_n_lines n="34" delta="10" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
182 <has_text text="Test Report Title"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
183 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
184 </output> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
185 </test> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
186 <!-- Test region literal option--> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
187 <test expect_num_outputs="2"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
188 <conditional name="reference_genome"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
189 <param name="source" value="history"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
190 <param name="history_item" value="reference.fasta"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
191 </conditional> |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
192 <param name="reads" value="reads.bam" ftype="bam"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
193 <param name="model_type" value="WGS"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
194 <conditional name="regions_conditional"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
195 <param name="regions_option" value="region"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
196 <param name="region_literal" value="K03455:1-2669"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
197 </conditional> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
198 <section name="advanced_options"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
199 <param name="vcf_stats_report" value="True"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
200 </section> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
201 <output name="vcf_file" ftype="vcf"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
202 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
203 <has_text text="#CHROM"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
204 <has_text text="##fileformat=VCFv4.2"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
205 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
206 </output> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
207 <output name="html_report" ftype="html"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
208 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
209 <is_valid_xml /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
210 <has_n_lines n="34" delta="10" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
211 <has_text text="Variant types"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
212 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
213 </output> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
214 </test> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
215 <!-- Test region bed option--> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
216 <test expect_num_outputs="2"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
217 <conditional name="reference_genome"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
218 <param name="source" value="history"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
219 <param name="history_item" value="reference.fasta"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
220 </conditional> |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
221 <param name="reads" value="reads.bam" ftype="bam"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
222 <param name="model_type" value="WGS"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
223 <conditional name="regions_conditional"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
224 <param name="regions_option" value="bed"/> |
|
2
98fe794d2ec0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 4255237ed7a51299e25bd7de7ad52ac5d419a56c
iuc
parents:
1
diff
changeset
|
225 <param name="bed_file" value="region.bed" ftype="bed"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
226 </conditional> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
227 <section name="advanced_options"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
228 <param name="vcf_stats_report" value="True"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
229 </section> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
230 <output name="vcf_file" ftype="vcf"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
231 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
232 <has_text text="#CHROM"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
233 <has_text text="##fileformat=VCFv4.2"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
234 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
235 </output> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
236 <output name="html_report" ftype="html"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
237 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
238 <is_valid_xml /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
239 <has_n_lines n="34" delta="10" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
240 <has_text text="Variant types"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
241 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
242 </output> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
243 </test> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
244 <!-- Test gvcf output option--> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
245 <test expect_num_outputs="3"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
246 <conditional name="reference_genome"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
247 <param name="source" value="history"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
248 <param name="history_item" value="reference.fasta"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
249 </conditional> |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
250 <param name="reads" value="reads.bam" ftype="bam"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
251 <param name="model_type" value="WGS"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
252 <param name="output_gvcf" value="True"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
253 <conditional name="regions_conditional"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
254 <param name="regions_option" value="region"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
255 <param name="region_literal" value="K03455:1-2669"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
256 </conditional> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
257 <section name="advanced_options"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
258 <param name="vcf_stats_report" value="True"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
259 </section> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
260 <output name="vcf_file" ftype="vcf"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
261 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
262 <has_text text="#CHROM"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
263 <has_text text="##fileformat=VCFv4.2"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
264 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
265 </output> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
266 <output name="gvcf_file" ftype="vcf"> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
267 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
268 <has_text text="#CHROM"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
269 <has_text text="##fileformat=VCFv4.2"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
270 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
271 </output> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
272 <output name="html_report" ftype="html"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
273 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
274 <is_valid_xml /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
275 <has_n_lines n="34" delta="10" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
276 <has_text text="Variant types"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
277 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
278 </output> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
279 </test> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
280 <!-- Test CRAM format input--> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
281 <test expect_num_outputs="2"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
282 <conditional name="reference_genome"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
283 <param name="source" value="history"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
284 <param name="history_item" value="reference.fasta"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
285 </conditional> |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
286 <param name="reads" value="reads.cram" ftype="cram"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
287 <param name="model_type" value="WGS"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
288 <conditional name="regions_conditional"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
289 <param name="regions_option" value="disabled"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
290 </conditional> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
291 <section name="advanced_options"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
292 <param name="vcf_stats_report" value="True"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
293 </section> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
294 <output name="vcf_file" ftype="vcf"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
295 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
296 <has_text text="#CHROM"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
297 <has_text text="##fileformat=VCFv4.2"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
298 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
299 </output> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
300 <output name="html_report" ftype="html"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
301 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
302 <is_valid_xml /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
303 <has_n_lines n="34" delta="10" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
304 <has_text text="Variant types"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
305 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
306 </output> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
307 </test> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
308 <!-- Test indexed reference format input--> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
309 <test expect_num_outputs="2"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
310 <conditional name="reference_genome"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
311 <param name="source" value="indexed"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
312 <param name="index" value="phix174"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
313 </conditional> |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
314 <param name="reads" value="reads.bam" ftype="bam"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
315 <param name="model_type" value="WGS"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
316 <conditional name="regions_conditional"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
317 <param name="regions_option" value="disabled"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
318 </conditional> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
319 <section name="advanced_options"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
320 <param name="vcf_stats_report" value="True"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
321 </section> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
322 <output name="vcf_file" ftype="vcf"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
323 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
324 <has_text text="#CHROM"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
325 <has_text text="##fileformat=VCFv4.2"/> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
326 </assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
327 </output> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
328 <output name="html_report" ftype="html"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
329 <assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
330 <is_valid_xml /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
331 <has_n_lines n="34" delta="10" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
332 <has_text text="Variant types"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
333 </assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
334 </output> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
335 </test> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
336 <!-- Test runtime report output--> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
337 <test expect_num_outputs="3"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
338 <conditional name="reference_genome"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
339 <param name="source" value="history"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
340 <param name="history_item" value="reference.fasta"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
341 </conditional> |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
342 <param name="reads" value="reads.bam" ftype="bam"/> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
343 <param name="model_type" value="WGS"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
344 <conditional name="regions_conditional"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
345 <param name="regions_option" value="disabled"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
346 </conditional> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
347 <section name="advanced_options"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
348 <param name="vcf_stats_report" value="True"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
349 <param name="create_runtime_report" value="True"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
350 </section> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
351 <output name="vcf_file" ftype="vcf"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
352 <assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
353 <has_text text="#CHROM"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
354 <has_text text="##fileformat=VCFv4.2"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
355 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
356 </output> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
357 <output name="html_report" ftype="html"> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
358 <assert_contents> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
359 <is_valid_xml /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
360 <has_n_lines n="34" delta="10" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
361 <has_text text="Variant types"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
362 </assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
363 </output> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
364 <output name="runtime_report" ftype="html"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
365 <assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
366 <is_valid_xml /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
367 <has_text text="Overall runtime"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
368 </assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
369 </output> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
370 </test> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
371 <!-- Test haploid contigs and PAR regions BED--> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
372 <test expect_num_outputs="2"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
373 <conditional name="reference_genome"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
374 <param name="source" value="history"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
375 <param name="history_item" value="reference.fasta"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
376 </conditional> |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
377 <param name="reads" value="reads.bam" ftype="bam"/> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
378 <param name="model_type" value="WGS"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
379 <conditional name="regions_conditional"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
380 <param name="regions_option" value="disabled"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
381 </conditional> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
382 <section name="advanced_options"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
383 <param name="vcf_stats_report" value="True"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
384 <param name="haploid_contigs" value="K03455"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
385 <param name="par_regions_bed" value="phix174.par_regions.bed" ftype="bed"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
386 </section> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
387 <output name="vcf_file" ftype="vcf"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
388 <assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
389 <has_text text="#CHROM"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
390 <has_text text="##fileformat=VCFv4.2"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
391 </assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
392 </output> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
393 <output name="html_report" ftype="html"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
394 <assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
395 <is_valid_xml /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
396 <has_n_lines n="34" delta="10" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
397 <has_text text="Variant types"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
398 </assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
399 </output> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
400 </test> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
401 <!-- Test expert options extra-args--> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
402 <test expect_num_outputs="2"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
403 <conditional name="reference_genome"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
404 <param name="source" value="history"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
405 <param name="history_item" value="reference.fasta"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
406 </conditional> |
|
6
1ad55977a040
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit 07e6d5d6cc0615ea23d18df910ee6b278b9cb5df
iuc
parents:
5
diff
changeset
|
407 <param name="reads" value="reads.bam" ftype="bam"/> |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
408 <param name="model_type" value="WGS"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
409 <conditional name="regions_conditional"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
410 <param name="regions_option" value="disabled"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
411 </conditional> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
412 <section name="advanced_options"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
413 <param name="vcf_stats_report" value="True"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
414 </section> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
415 <section name="expert_options"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
416 <param name="make_examples_extra_args" value="min_base_quality=10"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
417 <param name="call_variants_extra_args" value="allow_empty_examples=true"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
418 <param name="postprocess_variants_extra_args" value="cnn_homref_call_min_gq=20.0"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
419 </section> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
420 <output name="vcf_file" ftype="vcf"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
421 <assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
422 <has_text text="#CHROM"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
423 <has_text text="##fileformat=VCFv4.2"/> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
424 </assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
425 </output> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
426 <output name="html_report" ftype="html"> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
427 <assert_contents> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
428 <is_valid_xml /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
429 <has_n_lines n="34" delta="10" /> |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
430 <has_text text="Variant types"/> |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
431 </assert_contents> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
432 </output> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
433 </test> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
434 </tests> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
435 <help><![CDATA[ |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
436 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
437 .. class:: infomark |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
438 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
439 **Purpose** |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
440 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
441 DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
442 |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
443 DeepVariant runs a pipeline of three steps: **make_examples**, **call_variants**, and **postprocess_variants**. The **Expert options** section exposes extra-args fields for each step. Use these only with parameters that are accepted by the corresponding DeepVariant binary (see `run_deepvariant --helpfull` and the subcommand help, e.g. `/opt/deepvariant/bin/make_examples --helpfull` in the container). |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
444 |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
445 DeepVariant supports germline variant-calling in diploid organisms. |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
446 |
|
5
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
447 - NGS (Illumina) data for either a `whole genome <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-case-study.md>`_ or `whole exome <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-exome-case-study.md>`_. |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
448 - PacBio HiFi data, see the `PacBio case study <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-pacbio-model-case-study.md>`_. |
|
fd52f65372c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
iuc
parents:
4
diff
changeset
|
449 - Hybrid PacBio HiFi + Illumina WGS, see the `hybrid case study <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-hybrid-case-study.md>`_. |
|
0
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
450 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
451 Please also note: |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
452 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
453 For somatic data or any other samples where the genotypes go beyond two copies of DNA, DeepVariant will not work out of the box because the only genotypes supported are hom-alt, het, and hom-ref. |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
454 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
455 The models included with DeepVariant are only trained on human data. For other organisms, see the blog post on `non-human variant-calling <https://google.github.io/deepvariant/posts/2018-12-05-improved-non-human-variant-calling-using-species-specific-deepvariant-models/>`_ for some possible pitfalls and how to handle them. |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
456 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
457 ---- |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
458 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
459 .. class:: infomark |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
460 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
461 **How DeepVariants works** |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
462 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
463 DeepVariant relies on `Nucleus <https://github.com/google/nucleus>`_, a library of Python and C++ code for reading and writing data in common genomics file formats (like SAM and VCF) designed for painless integration with the `TensorFlow <https://www.tensorflow.org/>`_ machine learning framework. Nucleus was built with DeepVariant in mind and open-sourced separately so it can be used by anyone in the genomics research community for other projects. See this blog post on `Using Nucleus and TensorFlow for DNA Sequencing Error Correction <https://google.github.io/deepvariant/posts/2019-01-31-using-nucleus-and-tensorflow-for-dna-sequencing-error-correction/>`_. |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
464 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
465 |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
466 ]]> </help> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
467 <expand macro="citations"/> |
|
7608209110d3
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff
changeset
|
468 </tool> |