deepvariant: deepvariant.xml annotate

annotate deepvariant.xml @ 4:09fff9439112 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35

author	iuc
date	Mon, 02 Feb 2026 12:34:03 +0000
parents	1a3c1f1a4d24
children

rev	line source
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	1 <tool id='deepvariant' name='DeepVariant' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='@PROFILE@'>
0 2036bbf304d6 "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>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	3 <macros>
2036bbf304d6 "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>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	5 </macros>
2036bbf304d6 "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' />
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	7 <expand macro='requirements' />
2036bbf304d6 "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[
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	9 ln -s '${reads}' reads_alignment.bam
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	10 && ln -s '${reads.metadata.bam_index}' reads_alignment.bam.bai
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	11 #if $regions_conditional.regions_option == 'bed'
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	12 && ln -s '${regions_conditional.bed_file}' region.bed
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	13 #end if
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	14 #if $par_regions_bed
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	15 && ln -s '${par_regions_bed}' par_regions.bed
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	16 #end if
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	17 #set $logging_dir_value = None
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	18 #if $create_runtime_report
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	19 #set $logging_dir_value = 'logging'
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	20 && mkdir -p '$logging_dir_value'
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	21 #end if
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	22 #if $reference_genome.source == 'history':
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	23 #set $ref_genome = 'reference.fasta'
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	24 && ln -s -f '${reference_genome.history_item}' $ref_genome
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	25 && samtools faidx $ref_genome
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	26 #else:
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	27 #set $ref_genome = $reference_genome.index.fields.path
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	28 #end if
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	29 && run_deepvariant
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	30 --model_type=$model_type
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	31 --ref=$ref_genome
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	32 --reads='reads_alignment.bam'
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	33 #if $sample_name
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	34 --sample_name '$sample_name'
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	35 #end if
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	36 --output_vcf='./output.vcf.gz'
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	37 #if $output_gvcf
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	38 --output_gvcf='./output.g.vcf.gz'
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	39 #end if
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	40 #if $regions_conditional.regions_option == 'region'
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	41 --regions '$regions_conditional.region_literal'
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	42 #else if $regions_conditional.regions_option == 'bed'
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	43 --regions 'region.bed'
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	44 #end if
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	45 --disable_small_model=$disable_small_model
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	46 #if $haploid_contigs
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	47 --haploid_contigs='$haploid_contigs'
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	48 #end if
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	49 #if $par_regions_bed
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	50 --par_regions_bed='par_regions.bed'
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	51 #end if
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	52 #if $logging_dir_value
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	53 --logging_dir='$logging_dir_value'
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	54 #end if
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	55 #if $report_title
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	56 --report_title='$report_title'
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	57 #end if
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	58 --runtime_report=$create_runtime_report
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	59 #if $make_examples_extra_args
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	60 --make_examples_extra_args='$make_examples_extra_args'
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	61 #end if
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	62 #if $call_variants_extra_args
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	63 --call_variants_extra_args='$call_variants_extra_args'
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	64 #end if
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	65 #if $postprocess_variants_extra_args
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	66 --postprocess_variants_extra_args='$postprocess_variants_extra_args'
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	67 #end if
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	68 $vcf_stats_report
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	69 --num_shards=\${GALAXY_SLOTS:-2}
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	70 && gunzip './output.vcf.gz'
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	71 #if $output_gvcf
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	72 && gunzip './output.g.vcf.gz'
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	73 #end if
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	74 ]]> </command>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	75 <inputs>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	76 <conditional name="reference_genome">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	77 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	78 <option value="indexed" selected="true">Use a built-in genome</option>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	79 <option value="history">Use a genome from history</option>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	80 </param>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	81 <when value="indexed">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	82 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team.">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	83 <options from_data_table="fasta_indexes">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	84 <filter type="sort_by" column="2" />
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	85 <validator type="no_options" message="No genomes are available for the selected input dataset" />
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	86 </options>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	87 </param>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	88 </when>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	89 <when value="history">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	90 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	91 </when>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	92 </conditional>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	93 <param argument="--reads" type="data" format="bam" label="BAM file" help="An aligned reads file in BAM format. The reads must be aligned to the reference genome" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	94 <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 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	95 <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	96 <option value="WGS">WGS: Illumina whole genome sequencing</option>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	97 <option value="WES">WES: Illumina whole exome sequencing</option>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	98 <option value="PACBIO">PacBio HiFi</option>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	99 <option value="HYBRID_PACBIO_ILLUMINA">Hybrid PacBio HiFi-Illumina</option>
3 1a3c1f1a4d24 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1 iuc parents: 2 diff changeset	100 <option value="ONT_R104">ONT R10.4 simplex and duplex data</option>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	101 </param>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	102 <conditional name="regions_conditional">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	103 <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.">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	104 <option value="disabled" selected="True">Disabled</option>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	105 <option value="region">Specify region literals</option>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	106 <option value="bed">Provide a BED file</option>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	107 </param>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	108 <when value="disabled"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	109 <when value="region">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	110 <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'">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	111 <sanitizer invalid_char="">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	112 <valid initial="string.letters,string.digits">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	113 <add value="," />
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	114 <add value=":" />
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	115 <add value="-" />
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	116 </valid>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	117 </sanitizer>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	118 <validator type="regex">[0-9a-zA-Z,:-]+</validator>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	119 </param>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	120 </when>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	121 <when value="bed">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	122 <param name="bed_file" argument="--regions" type="data" format="bed" label="BED file" help="The BED should the store genomic regions of interest" />
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	123 </when>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	124 </conditional>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	125 <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" />
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	126 <section name="advanced_options" title="Advanced options" expanded="false">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	127 <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." />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	128 <param argument="--haploid_contigs" type="text" optional="true" label="Haploid contigs" help="Comma-separated list of non-autosomal chromosomes. Example: chrX,chrY" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	129 <param argument="--par_regions_bed" type="data" format="bed" optional="true" label="PAR regions BED file" help="BED file of pseudoautosomal regions." />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	130 <param argument="--report_title" type="text" optional="true" label="Report title" help="Title for the VCF stats report (HTML). Example: NA12878 DeepVariant report" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	131 <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." />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	132 <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." />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	133 </section>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	134 <section name="expert_options" title="Expert options (may increase runtime and disk usage)" expanded="false">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	135 <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" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	136 <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" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	137 <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" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	138 </section>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	139 </inputs>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	140 <outputs>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	141 <data name="vcf_file" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: VCF file"/>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	142 <data name="html_report" format="html" from_work_dir="output.visual_report.html" label="${tool.name} on ${on_string}: HTML report">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	143 <filter>advanced_options['vcf_stats_report']</filter>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	144 </data>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	145 <data name="runtime_report" format="html" from_work_dir="logging/make_examples_runtime_by_region_report.html" label="${tool.name} on ${on_string}: runtime report">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	146 <filter>advanced_options['create_runtime_report']</filter>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	147 </data>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	148 <data name="gvcf_file" format="vcf" from_work_dir="output.g.vcf" label="${tool.name} on ${on_string}: gVCF file">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	149 <filter>output_gvcf</filter>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	150 </data>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	151 </outputs>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	152 <tests>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	153 <test expect_num_outputs="2">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	154 <conditional name="reference_genome">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	155 <param name="source" value="history"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	156 <param name="history_item" value="reference.fasta"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	157 </conditional>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	158 <param name="reads" value="reads.bam"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	159 <param name="model_type" value="WGS"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	160 <param name="output_gvcf" value="False"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	161 <conditional name="regions_conditional">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	162 <param name="regions_option" value="disabled"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	163 </conditional>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	164 <section name="advanced_options">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	165 <param name="vcf_stats_report" value="True"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	166 <param name="report_title" value="Test Report Title"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	167 </section>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	168 <output name="vcf_file" ftype="vcf">
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	169 <assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	170 <has_text text="##fileformat=VCFv4.2"/>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	171 <has_text text="#CHROM"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	172 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	173 </output>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	174 <output name="html_report" ftype="html">
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	175 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	176 <is_valid_xml />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	177 <has_n_lines n="34" delta="10" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	178 <has_text text="Test Report Title"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	179 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	180 </output>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	181 </test>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	182 <!-- Test region literal option-->
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	183 <test expect_num_outputs="2">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	184 <conditional name="reference_genome">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	185 <param name="source" value="history"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	186 <param name="history_item" value="reference.fasta"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	187 </conditional>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	188 <param name="reads" value="reads.bam"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	189 <param name="model_type" value="WGS"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	190 <conditional name="regions_conditional">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	191 <param name="regions_option" value="region"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	192 <param name="region_literal" value="K03455:1-2669"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	193 </conditional>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	194 <section name="advanced_options">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	195 <param name="vcf_stats_report" value="True"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	196 </section>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	197 <output name="vcf_file" ftype="vcf">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	198 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	199 <has_text text="#CHROM"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	200 <has_text text="##fileformat=VCFv4.2"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	201 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	202 </output>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	203 <output name="html_report" ftype="html">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	204 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	205 <is_valid_xml />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	206 <has_n_lines n="34" delta="10" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	207 <has_text text="Variant types"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	208 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	209 </output>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	210 </test>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	211 <!-- Test region bed option-->
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	212 <test expect_num_outputs="2">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	213 <conditional name="reference_genome">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	214 <param name="source" value="history"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	215 <param name="history_item" value="reference.fasta"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	216 </conditional>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	217 <param name="reads" value="reads.bam"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	218 <param name="model_type" value="WGS"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	219 <conditional name="regions_conditional">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	220 <param name="regions_option" value="bed"/>
2 1071eaa424a2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 4255237ed7a51299e25bd7de7ad52ac5d419a56c iuc parents: 1 diff changeset	221 <param name="bed_file" value="region.bed" ftype="bed"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	222 </conditional>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	223 <section name="advanced_options">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	224 <param name="vcf_stats_report" value="True"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	225 </section>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	226 <output name="vcf_file" ftype="vcf">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	227 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	228 <has_text text="#CHROM"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	229 <has_text text="##fileformat=VCFv4.2"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	230 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	231 </output>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	232 <output name="html_report" ftype="html">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	233 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	234 <is_valid_xml />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	235 <has_n_lines n="34" delta="10" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	236 <has_text text="Variant types"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	237 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	238 </output>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	239 </test>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	240 <!-- Test gvcf output option-->
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	241 <test expect_num_outputs="3">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	242 <conditional name="reference_genome">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	243 <param name="source" value="history"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	244 <param name="history_item" value="reference.fasta"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	245 </conditional>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	246 <param name="reads" value="reads.bam"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	247 <param name="model_type" value="WGS"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	248 <param name="output_gvcf" value="True"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	249 <conditional name="regions_conditional">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	250 <param name="regions_option" value="region"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	251 <param name="region_literal" value="K03455:1-2669"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	252 </conditional>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	253 <section name="advanced_options">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	254 <param name="vcf_stats_report" value="True"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	255 </section>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	256 <output name="vcf_file" ftype="vcf">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	257 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	258 <has_text text="#CHROM"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	259 <has_text text="##fileformat=VCFv4.2"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	260 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	261 </output>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	262 <output name="gvcf_file" ftype="vcf">
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	263 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	264 <has_text text="#CHROM"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	265 <has_text text="##fileformat=VCFv4.2"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	266 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	267 </output>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	268 <output name="html_report" ftype="html">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	269 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	270 <is_valid_xml />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	271 <has_n_lines n="34" delta="10" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	272 <has_text text="Variant types"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	273 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	274 </output>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	275 </test>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	276 <!-- Test CRAM format input-->
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	277 <test expect_num_outputs="2">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	278 <conditional name="reference_genome">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	279 <param name="source" value="history"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	280 <param name="history_item" value="reference.fasta"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	281 </conditional>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	282 <param name="reads" value="reads.cram"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	283 <param name="model_type" value="WGS"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	284 <conditional name="regions_conditional">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	285 <param name="regions_option" value="disabled"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	286 </conditional>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	287 <section name="advanced_options">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	288 <param name="vcf_stats_report" value="True"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	289 </section>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	290 <output name="vcf_file" ftype="vcf">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	291 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	292 <has_text text="#CHROM"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	293 <has_text text="##fileformat=VCFv4.2"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	294 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	295 </output>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	296 <output name="html_report" ftype="html">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	297 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	298 <is_valid_xml />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	299 <has_n_lines n="34" delta="10" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	300 <has_text text="Variant types"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	301 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	302 </output>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	303 </test>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	304 <!-- Test indexed reference format input-->
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	305 <test expect_num_outputs="2">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	306 <conditional name="reference_genome">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	307 <param name="source" value="indexed"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	308 <param name="index" value="phix174"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	309 </conditional>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	310 <param name="reads" value="reads.bam"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	311 <param name="model_type" value="WGS"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	312 <conditional name="regions_conditional">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	313 <param name="regions_option" value="disabled"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	314 </conditional>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	315 <section name="advanced_options">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	316 <param name="vcf_stats_report" value="True"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	317 </section>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	318 <output name="vcf_file" ftype="vcf">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	319 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	320 <has_text text="#CHROM"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	321 <has_text text="##fileformat=VCFv4.2"/>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	322 </assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	323 </output>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	324 <output name="html_report" ftype="html">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	325 <assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	326 <is_valid_xml />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	327 <has_n_lines n="34" delta="10" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	328 <has_text text="Variant types"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	329 </assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	330 </output>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	331 </test>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	332 <!-- Test runtime report output-->
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	333 <test expect_num_outputs="3">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	334 <conditional name="reference_genome">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	335 <param name="source" value="history"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	336 <param name="history_item" value="reference.fasta"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	337 </conditional>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	338 <param name="reads" value="reads.bam"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	339 <param name="model_type" value="WGS"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	340 <conditional name="regions_conditional">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	341 <param name="regions_option" value="disabled"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	342 </conditional>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	343 <section name="advanced_options">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	344 <param name="vcf_stats_report" value="True"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	345 <param name="create_runtime_report" value="True"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	346 </section>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	347 <output name="vcf_file" ftype="vcf">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	348 <assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	349 <has_text text="#CHROM"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	350 <has_text text="##fileformat=VCFv4.2"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	351 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	352 </output>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	353 <output name="html_report" ftype="html">
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	354 <assert_contents>
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	355 <is_valid_xml />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	356 <has_n_lines n="34" delta="10" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	357 <has_text text="Variant types"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	358 </assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	359 </output>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	360 <output name="runtime_report" ftype="html">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	361 <assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	362 <is_valid_xml />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	363 <has_text text="Overall runtime"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	364 </assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	365 </output>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	366 </test>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	367 <!-- Test haploid contigs and PAR regions BED-->
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	368 <test expect_num_outputs="2">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	369 <conditional name="reference_genome">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	370 <param name="source" value="history"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	371 <param name="history_item" value="reference.fasta"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	372 </conditional>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	373 <param name="reads" value="reads.bam"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	374 <param name="model_type" value="WGS"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	375 <conditional name="regions_conditional">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	376 <param name="regions_option" value="disabled"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	377 </conditional>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	378 <section name="advanced_options">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	379 <param name="vcf_stats_report" value="True"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	380 <param name="haploid_contigs" value="K03455"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	381 <param name="par_regions_bed" value="phix174.par_regions.bed" ftype="bed"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	382 </section>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	383 <output name="vcf_file" ftype="vcf">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	384 <assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	385 <has_text text="#CHROM"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	386 <has_text text="##fileformat=VCFv4.2"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	387 </assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	388 </output>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	389 <output name="html_report" ftype="html">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	390 <assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	391 <is_valid_xml />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	392 <has_n_lines n="34" delta="10" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	393 <has_text text="Variant types"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	394 </assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	395 </output>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	396 </test>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	397 <!-- Test expert options extra-args-->
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	398 <test expect_num_outputs="2">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	399 <conditional name="reference_genome">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	400 <param name="source" value="history"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	401 <param name="history_item" value="reference.fasta"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	402 </conditional>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	403 <param name="reads" value="reads.bam"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	404 <param name="model_type" value="WGS"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	405 <conditional name="regions_conditional">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	406 <param name="regions_option" value="disabled"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	407 </conditional>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	408 <section name="advanced_options">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	409 <param name="vcf_stats_report" value="True"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	410 </section>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	411 <section name="expert_options">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	412 <param name="make_examples_extra_args" value="min_base_quality=10"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	413 <param name="call_variants_extra_args" value="allow_empty_examples=true"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	414 <param name="postprocess_variants_extra_args" value="cnn_homref_call_min_gq=20.0"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	415 </section>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	416 <output name="vcf_file" ftype="vcf">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	417 <assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	418 <has_text text="#CHROM"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	419 <has_text text="##fileformat=VCFv4.2"/>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	420 </assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	421 </output>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	422 <output name="html_report" ftype="html">
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	423 <assert_contents>
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	424 <is_valid_xml />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	425 <has_n_lines n="34" delta="10" />
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	426 <has_text text="Variant types"/>
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	427 </assert_contents>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	428 </output>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	429 </test>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	430 </tests>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	431 <help><![CDATA[
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	432
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	433 .. class:: infomark
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	434
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	435 Purpose
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	436
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	437 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.
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	438
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	439 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).
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	440
0 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	441 DeepVariant supports germline variant-calling in diploid organisms.
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	442
4 09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	443 - 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>`_.
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	444 - PacBio HiFi data, see the `PacBio case study <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-pacbio-model-case-study.md>`_.
09fff9439112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35 iuc parents: 3 diff changeset	445 - 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 2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	446
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	447 Please also note:
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	448
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	449 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.
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	450
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	451 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.
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	452
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	453 ----
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	454
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	455 .. class:: infomark
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	456
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	457 How DeepVariants works
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	458
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	459 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/>`_.
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	460
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	461
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	462 ]]> </help>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	463 <expand macro="citations"/>
2036bbf304d6 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe" iuc parents: diff changeset	464 </tool>

Mercurial > repos > iuc > deepvariant

annotate deepvariant.xml @ 4:09fff9439112 draft default tip