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annotate deepvariant.xml @ 3:918c8b94c8d8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
author iuc
date Mon, 10 Apr 2023 11:11:16 +0000
parents 98fe794d2ec0
children 63b68fe4af85
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7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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1 <tool id='deepvariant' name='DeepVariant' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='20.01'>
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2 <description>deep learning-based variant caller</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro='edam_ontology' />
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7 <expand macro='requirements' />
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8 <command detect_errors='exit_code'><![CDATA[
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9 ln -s '${reads}' reads_alignment.bam
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10 && ln -s '${reads.metadata.bam_index}' reads_alignment.bam.bai
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11 #if $regions_conditional.regions_option == 'bed'
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12 && ln -s '${regions_conditional.bed_file}' region.bed
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13 #end if
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
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14 #if $reference_genome.source == 'history':
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15 #set $ref_genome = 'reference.fasta'
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16 && ln -s -f '${reference_genome.history_item}' $ref_genome
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17 && samtools faidx $ref_genome
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18 #else:
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19 #set $ref_genome = $reference_genome.index.fields.path
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20 #end if
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21 && run_deepvariant
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22 --model_type=$model_type
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23 --ref=$ref_genome
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24 --reads=reads_alignment.bam
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25 --output_vcf='./output.vcf.gz'
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26 #if $output_gvcf
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27 --output_gvcf='./output.g.vcf.gz'
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28 #end if
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29 #if $regions_conditional.regions_option == 'region'
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30 --regions $regions_conditional.region_literal
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31 #else if $regions_conditional.regions_option == 'bed'
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32 --regions region.bed
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33 #end if
1
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34 ##--call_variants_extra_args="use_openvino=true" ## Setting this will use OpenVINO on Intel CPUs, which empirically reduces call_variants runtime by 15%-25%.
0
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35 --num_shards=\${GALAXY_SLOTS:-2}
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36 && gunzip './output.vcf.gz'
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37 #if $output_gvcf
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38 && gunzip './output.g.vcf.gz'
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39 #end if
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40 ]]> </command>
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41 <inputs>
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42 <conditional name="reference_genome">
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43 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">
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44 <option value="indexed" selected="true">Use a built-in genome</option>
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45 <option value="history">Use a genome from history</option>
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46 </param>
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47 <when value="indexed">
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48 <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team.">
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49 <options from_data_table="fasta_indexes">
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50 <filter type="sort_by" column="2" />
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51 <validator type="no_options" message="No genomes are available for the selected input dataset" />
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52 </options>
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53 </param>
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54 </when>
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55 <when value="history">
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56 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
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57 </when>
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58 </conditional>
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59 <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" />
0
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60 <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling">
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61 <option value="WGS">WGS: Illumina whole genome sequencing</option>
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62 <option value="WES">WES: Illumina whole exome sequencing</option>
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63 <option value="PACBIO">PacBio HiFi</option>
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64 <option value="HYBRID_PACBIO_ILLUMINA">Hybrid PacBio HiFi-Illumina</option>
3
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65 <option value="ONT_R104">ONT R10.4 simplex and duplex data</option>
0
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66 </param>
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67 <conditional name="regions_conditional">
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68 <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.">
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69 <option value="disabled" selected="True">Disabled</option>
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70 <option value="region">Specify region literals</option>
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71 <option value="bed">Provide a BED file</option>
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72 </param>
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73 <when value="disabled"/>
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74 <when value="region">
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75 <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'">
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76 <sanitizer invalid_char="">
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77 <valid initial="string.letters,string.digits">
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78 <add value="," />
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79 <add value=":" />
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80 <add value="-" />
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81 </valid>
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82 </sanitizer>
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83 <validator type="regex">[0-9a-zA-Z,:-]+</validator>
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84 </param>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
85 </when>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
86 <when value="bed">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
87 <param name="bed_file" argument="--regions" type="data" format="bed" label="BED file" help="The BED should the store genomic regions of interest" />
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
88 </when>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
89 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
90 <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" />
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
91 </inputs>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
92 <outputs>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
93 <data name="vcf_file" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: VCF file"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
94 <data name="html_report" format="html" from_work_dir="output.visual_report.html" label="${tool.name} on ${on_string}: HTML report"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
95 <data name="gvcf_file" format="vcf" from_work_dir="output.g.vcf" label="${tool.name} on ${on_string}: gVCF file">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
96 <filter>output_gvcf</filter>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
97 </data>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
98 </outputs>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
99 <tests>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
100 <test expect_num_outputs="2">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
101 <conditional name="reference_genome">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
102 <param name="source" value="history"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
103 <param name="history_item" value="reference.fasta"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
104 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
105 <param name="reads" value="reads.bam"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
106 <param name="model_type" value="WGS"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
107 <param name="output_gvcf" value="False"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
108 <conditional name="regions_conditional">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
109 <param name="regions_option" value="disabled"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
110 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
111 <output name="vcf_file" file="output.vcf" ftype="vcf">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
112 <assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
113 <has_text text="##fileformat=VCFv4.2"/>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
114 <has_size value="2478" delta="10"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
115 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
116 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
117 <output name="html_report" file="report.html" ftype="html">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
118 <assert_contents>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
119 <has_size value="23176" delta="100"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
120 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
121 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
122 </test>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
123 <!-- Test region literal option-->
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
124 <test expect_num_outputs="2">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
125 <conditional name="reference_genome">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
126 <param name="source" value="history"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
127 <param name="history_item" value="reference.fasta"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
128 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
129 <param name="reads" value="reads.bam"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
130 <param name="model_type" value="WGS"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
131 <conditional name="regions_conditional">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
132 <param name="regions_option" value="region"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
133 <param name="region_literal" value="K03455:1-2669"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
134 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
135 <output name="vcf_file" ftype="vcf">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
136 <assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
137 <has_text text="##fileformat=VCFv4.2"/>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
138 <has_size value="1843" delta="10"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
139 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
140 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
141 <output name="html_report" ftype="html">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
142 <assert_contents>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
143 <has_size value="18894" delta="100"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
144 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
145 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
146 </test>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
147 <!-- Test region bed option-->
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
148 <test expect_num_outputs="2">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
149 <conditional name="reference_genome">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
150 <param name="source" value="history"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
151 <param name="history_item" value="reference.fasta"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
152 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
153 <param name="reads" value="reads.bam"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
154 <param name="model_type" value="WGS"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
155 <conditional name="regions_conditional">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
156 <param name="regions_option" value="bed"/>
2
98fe794d2ec0 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 4255237ed7a51299e25bd7de7ad52ac5d419a56c
iuc
parents: 1
diff changeset
157 <param name="bed_file" value="region.bed" ftype="bed"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
158 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
159 <output name="vcf_file" ftype="vcf">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
160 <assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
161 <has_text text="##fileformat=VCFv4.2"/>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
162 <has_size value="1843" delta="10"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
163 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
164 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
165 <output name="html_report" ftype="html">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
166 <assert_contents>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
167 <has_size value="18894" delta="100"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
168 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
169 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
170 </test>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
171 <!-- Test gvcf output option-->
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
172 <test expect_num_outputs="3">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
173 <conditional name="reference_genome">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
174 <param name="source" value="history"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
175 <param name="history_item" value="reference.fasta"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
176 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
177 <param name="reads" value="reads.bam"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
178 <param name="model_type" value="WGS"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
179 <param name="output_gvcf" value="True"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
180 <conditional name="regions_conditional">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
181 <param name="regions_option" value="region"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
182 <param name="region_literal" value="K03455:1-2669"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
183 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
184 <output name="vcf_file" ftype="vcf">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
185 <assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
186 <has_text text="##fileformat=VCFv4.2"/>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
187 <has_size value="1843" delta="10"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
188 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
189 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
190 <output name="gvcf_file" file="output.g.vcf" ftype="vcf">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
191 <assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
192 <has_text text="##fileformat=VCFv4.2"/>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
193 <has_size value="3192" delta="10" />
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
194 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
195 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
196 <output name="html_report" ftype="html">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
197 <assert_contents>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
198 <has_size value="18894" delta="100"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
199 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
200 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
201 </test>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
202 <!-- Test CRAM format input-->
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
203 <test expect_num_outputs="2">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
204 <conditional name="reference_genome">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
205 <param name="source" value="history"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
206 <param name="history_item" value="reference.fasta"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
207 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
208 <param name="reads" value="reads.cram"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
209 <param name="model_type" value="WGS"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
210 <conditional name="regions_conditional">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
211 <param name="regions_option" value="disabled"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
212 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
213 <output name="vcf_file" ftype="vcf">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
214 <assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
215 <has_text text="##fileformat=VCFv4.2"/>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
216 <has_size value="2478"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
217 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
218 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
219 <output name="html_report" ftype="html">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
220 <assert_contents>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
221 <has_size value="23176" delta="100"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
222 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
223 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
224 </test>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
225 <!-- Test indexed reference format input-->
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
226 <test expect_num_outputs="2">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
227 <conditional name="reference_genome">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
228 <param name="source" value="indexed"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
229 <param name="index" value="phix174"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
230 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
231 <param name="reads" value="reads.bam"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
232 <param name="model_type" value="WGS"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
233 <conditional name="regions_conditional">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
234 <param name="regions_option" value="disabled"/>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
235 </conditional>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
236 <output name="vcf_file" ftype="vcf">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
237 <assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
238 <has_text text="##fileformat=VCFv4.2"/>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
239 <has_size value="2478"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
240 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
241 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
242 <output name="html_report" ftype="html">
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
243 <assert_contents>
3
918c8b94c8d8 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit 95f18cd38ca051a3f5cfe456c1a8ef5fa21730d1
iuc
parents: 2
diff changeset
244 <has_size value="23176" delta="100"/>
0
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
245 </assert_contents>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
246 </output>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
247 </test>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
248 </tests>
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
249 <help><![CDATA[
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
250
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
251 .. class:: infomark
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
252
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
253 **Purpose**
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
254
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
255 DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
256
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
257 DeepVariant supports germline variant-calling in diploid organisms.
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
258
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
259 - NGS (Illumina) data for either a `whole genome <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-case-study.md>`_ or `whole exome <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-exome-case-study.md>`_.
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
parents:
diff changeset
260 - PacBio HiFi data, see the `PacBio case study <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-pacbio-model-case-study.md>`_.
7608209110d3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/deepvariant commit e46feb5432b28a9360a1d4e8a6618e6ed91008fe"
iuc
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261 - Hybrid PacBio HiFi + Illumina WGS, see the `hybrid case study <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-hybrid-case-study.md>`_.
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262
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263 Please also note:
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264
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265 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.
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266
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267 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.
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268
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269 ----
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270
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271 .. class:: infomark
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272
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273 **How DeepVariants works**
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274
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275 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/>`_.
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276
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277
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278 ]]> </help>
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279 <expand macro="citations"/>
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280 </tool>