Mercurial > repos > iuc > clair3

annotate clair3.xml @ 1:63e02ef6e153 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
author iuc
date Fri, 28 Oct 2022 20:58:30 +0000
parents 44f6ec903688
children
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44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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1 <tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09">
1
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
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2 <description>germline small variant caller for long-reads</description>
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3 <macros>
1
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4 <token name="@TOOL_VERSION@">0.1.12</token>
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5 <token name="@VERSION_SUFFIX@">0</token>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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6 </macros>
1
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7 <xrefs>
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8 <xref type='bio.tools'>clair3</xref>
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9 </xrefs>
0
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10 <requirements>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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11 <requirement type="package" version="@TOOL_VERSION@">clair3</requirement>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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12 </requirements>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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13 <version_command><![CDATA[run_clair3.sh --version | cut -f2 -d ' ']]></version_command>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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14 <command detect_errors="exit_code"><![CDATA[
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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15 #if $ref_source.source == "history"
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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16 ln -s '${ref_source.ref_fasta}' reference.fasta &&
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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17 #elif $ref_source.source == "builtin"
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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18 ln -s '${ref_source.ref_fasta_builtin.fields.path}' reference.fasta &&
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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19 #end if
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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20 samtools faidx reference.fasta &&
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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21
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22 #if $model_source.source == "datatable"
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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23 #set model_path = $model_source.model.fields.path
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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24 #end if
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25 #set $extension = $bam_input.ext
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
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26 ln -s '${$bam_input}' input_reads.$extension &&
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
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27 #if $extension == 'bam'
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
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28 ln -s '${$bam_input.metadata.bam_index}' input_reads.bai &&
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
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29 #else
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30 ln -s '${$bam_input.metadata.cram_index}' input_reads.crai &&
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
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31 #end if
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32
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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33 #if $bed_or_vcf.bed_or_vcf_selector == 'bed'
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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34 ln -s '$bed_or_vcf.bed_fn' input.bed &&
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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35 #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf'
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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36 ln -s '$bed_or_vcf.vcf_fn' input.vcf &&
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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37 #end if
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38
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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39 run_clair3.sh
1
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40 --bam_fn=input_reads.$extension
0
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41 --ref_fn=reference.fasta
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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42 #if $model_source.source == "datatable"
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43 --platform='${model_source.model.fields.platform}'
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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44 --model_path=${model_source.model.fields.path}
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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45 #else
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46 #if $model_source.select_built_in == "hifi" or $model_source.select_built_in == "ilmn":
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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47 --platform='${$model_source.select_built_in}'
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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48 #else
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49 --platform='ont'
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50 #end if
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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51 --model_path=\$(dirname \$(which run_clair3.sh))/models/$model_source.select_built_in
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52 #end if
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53 --output='.'
1
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54 --threads=\${GALAXY_SLOTS:-2}
0
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55 #if $bed_or_vcf.bed_or_vcf_selector == 'bed'
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56 --bed_fn=input.bed
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57 #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf'
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58 --vcf_fn=input.vcf
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59 #else
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60 $bed_or_vcf.include_all_ctgs
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61 #end if
1
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62 $gvcf
0
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63 #if $adv.qual
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64 --qual=$adv.qual
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65 #end if
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66 #if $adv.snp_min_af
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67 --snp_min_af=$adv.snp_min_af
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68 #end if
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69 #if $adv.indel_min_af
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70 --indel_min_af=$adv.indel_min_af
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71 #end if
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72 $adv.enable_phasing
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73 $adv.no_phasing_for_fa
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74 $adv.print_ref_calls
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75 $adv.ploidity_model
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76 #if $adv.chunk_size
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77 --chunk_size=$adv.chunk_size
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78 #end if
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79
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80 ]]></command>
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81 <inputs>
1
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82 <param type="data" name="bam_input" argument="--bam_fn" format="bam,cram" label="BAM/CRAM file input" />
0
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83 <conditional name="ref_source">
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84 <param type="select" label="Reference genome source" name="source">
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85 <option value="history" selected="true">History</option>
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86 <option value="builtin">Built-in</option>
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87 </param>
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88 <when value="history">
1
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89 <param type="data" format="fasta" name="ref_fasta" argument="--ref_fn" label="Reference genome" />
0
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90 </when>
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91 <when value="builtin">
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92 <param type="select" name="ref_fasta_builtin" label="Reference genome">
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93 <options from_data_table="all_fasta" />
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94 </param>
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95 </when>
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96 </conditional>
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97 <conditional name="model_source">
1
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98 <param name="source" type="select" label="Clair3 model" help="Select if you want to use a built-in model shipping with the tool or a model cached on this Galaxy server.">
0
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99 <option value="built-in">Built-in</option>
1
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100 <option value="datatable">Cached</option>
0
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101 </param>
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102 <when value="built-in">
1
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103 <param type="select" name="select_built_in" label="Built-in model">
0
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104 <option value="r941_prom_sup_g5014">r941_prom_sup_g5014</option>
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105 <option value="r941_prom_hac_g360+g422">r941_prom_hac_g360+g422</option>
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106 <option value="hifi">hifi</option>
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107 <option value="ilmn">ilmn</option>
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108 </param>
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109 </when>
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110 <when value="datatable">
1
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111 <param name="model" argument="--model_path" type="select" label="Cached model from server" >
0
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112 <options from_data_table="clair3_models">
1
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113 <validator type="no_options" message="no cached models available" />
0
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114 </options>
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115 </param>
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116 </when>
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117 </conditional>
1
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118 <conditional name="bed_or_vcf">
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119 <param type="select" name="bed_or_vcf_selector" label="Restict variant calling to:">
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120 <option value="unrestricted" selected="true">Whole reference (unrestricted)</option>
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121 <option value="bed" selected="true">Regions defined in BED dataset</option>
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122 <option value="vcf">Sites defined in VCF dataset</option>
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123 </param>
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124 <when value="bed">
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125 <param type="data" argument="--bed_fn" format="bed" label="Call variants only in the provided bed regions."/>
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126 </when>
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127 <when value="vcf">
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128 <param type="data" argument="--vcf_fn" format="vcf" label="Candidate sites VCF file input" help="Variants will only be called at the sites in the VCF file if provided."/>
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129 </when>
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130 <when value="unrestricted">
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131 <param type="boolean" argument="--include_all_ctgs" truevalue="--include_all_ctgs" falsevalue="" checked="true" label="Call variants on all contigs" help="If disabled, call in chr{1..22,X,Y} and {1..22,X,Y}" />
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132 </when>
0
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133 </conditional>
1
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134 <param type="boolean" argument="--gvcf" truevalue="--gvcf" falsevalue="" label="Enable GVCF output" help="GVCF stands for Genomic VCF. A GVCF is a kind of VCF, so the basic format specification is the same as for a regular VCF but contains extra information. Default: disable" />
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135 <param name="output_files" type="select" display="checkboxes" multiple="true" label="Optional additional output files">
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136 <option value="full_alignment">Full alignment file</option>
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137 <option value="pileup">Pileup file</option>
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138 <option value="phased_bam">Phased BAM file</option>
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139 </param>
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140 <section name="adv" title="Advanced parameters" expanded="false">
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141 <param type="integer" argument="--qual" value="0" min="0" label="Qual" help="If set, variants with >qual will be marked PASS, or LowQual otherwise." />
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142 <param type="float" argument="--snp_min_af" value="0.08" min="0" max="1" label="Minimum SNP AF" help="Minimum SNP AF required for a candidate variant. Lowering the value might increase a bit of sensitivity in trade of speed and accuracy. Default: ont:0.08,hifi:0.08,ilmn:0.08." />
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143 <param type="float" argument="--indel_min_af" value="0.15" min="0" max="1" label="Minimum INDEL AF" help="Minimum INDEL AF required for a candidate variant. Lowering the value might increase a bit of sensitivity in trade of speed and accuracy. Default: ont:0.15,hifi:0.08,ilmn:0.08." />
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144 <param type="boolean" argument="--enable_phasing" truevalue="--enable_phasing" falsevalue="" label="Enable phasing" help="Output phased variants using whatshap. Default: disable" />
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145 <param type="boolean" argument="--no_phasing_for_fa" truevalue="--no_phasing_for_fa" falsevalue="" label="Call variants without whatshap phasing" help="EXPERIMENTAL: Call variants without whatshap phasing in full alignment calling. Default: disable" />
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146 <param type="boolean" argument="--print_ref_calls" truevalue="--print_ref_calls" falsevalue="" label="Print reference calls" help="Show reference calls (0/0) in vcf file. Default: disable." />
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147 <param type="select" name="ploidity_model" label="Call with the following ploidy model" help="EXPERIMENTAL. When haploid sensitive is enabled only 1/1 is considered as a variant. When haploid precise is enabled only 0/1 and 1/1 are considered as a variant. Default: diploid.">
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148 <option value="" selected="true">Diploid</option>
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149 <option value="--haploid_sensitive">Haploid sensitive (--haploid_sensitive)</option>
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150 <option value="--haploid_precise">haploid precise (--haploid_precise)</option>
0
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151 </param>
1
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152 <param type="integer" argument="--chunk_size" value="5000000" min="1" label="Chunk size" help="The size of each chuck for parallel processing. Default: 5Mbp." optional="true" />
0
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153 </section>
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154 </inputs>
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155 <outputs>
1
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156 <data name="merge_output" format="vcf_bgzip" from_work_dir="./merge_output.vcf.gz" label="${tool.name} on ${on_string}: merged output"/>
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157 <data name="pileup" format="vcf_bgzip" from_work_dir="./pileup.vcf.gz" label="${tool.name} on ${on_string}: pileup">
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158 <filter>output_files and 'pileup' in output_files</filter>
0
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159 </data>
1
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160 <data name="full_alignment" format="vcf_bgzip" from_work_dir="./full_alignment.vcf.gz" label="${tool.name} on ${on_string}: full alignment">
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161 <filter>output_files and 'full_alignment' in output_files</filter>
0
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162 </data>
1
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163 <data name="phased_bam" format="bam" from_work_dir="./phased_bam.bam" label="${tool.name} on ${on_string}: phased BAM">
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164 <filter>output_files and 'phased_bam' in output_files</filter>
0
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165 </data>
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166 </outputs>
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167 <tests>
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168 <test expect_num_outputs="1">
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169 <conditional name="model_source">
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170 <param name="source" value="built-in"/>
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171 <param name="select_built_in" value="r941_prom_hac_g360+g422"/>
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172 </conditional>
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173 <param name="bam_input" value="test1.bam" />
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174 <conditional name="ref_source">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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175 <param name="source" value="history" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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176 <param name="ref_fasta" value="test1.fasta" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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177 </conditional>
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178 <conditional name="bed_or_vcf">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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179 <param name="bed_or_vcf_selector" value="vcf"/>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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180 <param name="vcf_fn" value="test1.vcf.gz" />
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181 </conditional>
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182 <section name="adv">
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183 <param name="no_phasing_for_fa" value="true"/>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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184 <param name="print_ref_calls" value="true"/>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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185 <param name="ploidity_model" value=""/>
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186 </section>
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187 <assert_stdout>
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iuc
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188 <has_text text="[WARNING] No contig intersection found, output header only in" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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189 </assert_stdout>
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190 </test>
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191 <test expect_num_outputs="4">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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192 <conditional name="model_source">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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193 <param name="source" value="builtin" />
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194 <param name="select_built_in" value="r941_prom_hac_g360+g422" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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195 </conditional>
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196 <param name="bam_input" value="test1.bam" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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197 <conditional name="bed_or_vcf">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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198 <param name="bed_or_vcf_selector" value="unrestricted"/>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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199 <param name="include_all_ctgs" value="true" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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200 </conditional>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
201 <conditional name="ref_source">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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202 <param name="source" value="builtin" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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203 <param name="ref_fasta_builtin" value="test1" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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204 </conditional>
1
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iuc
parents: 0
diff changeset
205 <param name="gvcf" value="true"/>
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
iuc
parents: 0
diff changeset
206 <param name="output_files" value="full_alignment,pileup,phased_bam"/>
0
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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207 <section name="adv">
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208 <param name="print_ref_calls" value="true"/>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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209 </section>
1
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
iuc
parents: 0
diff changeset
210 <output name="merge_output" decompress="true" file="merge_output_1.vcf.gz" ftype="vcf_bgzip"/>
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
iuc
parents: 0
diff changeset
211 <output name="pileup" decompress="true" file="pileup_1.vcf.gz" ftype="vcf_bgzip"/>
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
iuc
parents: 0
diff changeset
212 <output name="full_alignment" decompress="true" file="full_alignment_1.vcf.gz" ftype="vcf_bgzip"/>
0
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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213 <output name="phased_bam" file="phased_bam_1.bam" ftype="bam"/>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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214 </test>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
215 <test expect_num_outputs="4">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
216 <conditional name="model_source">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
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217 <param name="source" value="datatable" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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218 <param name="model" value="test_model" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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219 </conditional>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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220 <param name="bam_input" value="test1.bam" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
221 <conditional name="bed_or_vcf">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
222 <param name="bed_or_vcf_selector" value="bed"/>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
223 <param name="bed_fn" value="test1.bed" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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224 </conditional>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
225 <conditional name="ref_source">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
226 <param name="source" value="builtin" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
227 <param name="ref_fasta_builtin" value="test1" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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228 </conditional>
1
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
iuc
parents: 0
diff changeset
229 <param name="output_files" value="full_alignment,pileup,phased_bam"/>
0
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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diff changeset
230 <section name="adv">
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iuc
parents:
diff changeset
231 <param name="snp_min_af" value="0.5"/>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
232 <param name="indel_min_af" value="0.12"/>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
233 <param name="no_phasing_for_fa" value="true" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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234 <param name="print_ref_calls" value="true"/>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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diff changeset
235 </section>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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diff changeset
236 <output name="merge_output" ftype="vcf_bgzip">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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237 <assert_contents>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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238 <has_size value="450" delta="50" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
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239 </assert_contents>
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240 </output>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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241 <output name="pileup" ftype="vcf_bgzip">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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242 <assert_contents>
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iuc
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diff changeset
243 <has_size value="0" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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244 </assert_contents>
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245 </output>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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246 <output name="full_alignment" ftype="vcf_bgzip">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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247 <assert_contents>
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iuc
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diff changeset
248 <has_size value="0" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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249 </assert_contents>
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iuc
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250 </output>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
251 <output name="phased_bam" ftype="bam">
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
252 <assert_contents>
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
parents:
diff changeset
253 <has_size value="0" />
44f6ec903688 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f
iuc
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254 </assert_contents>
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255 </output>
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iuc
parents:
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256 </test>
1
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iuc
parents: 0
diff changeset
257 <!-- Test input CRAM -->
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iuc
parents: 0
diff changeset
258 <test expect_num_outputs="1">
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iuc
parents: 0
diff changeset
259 <conditional name="model_source">
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
iuc
parents: 0
diff changeset
260 <param name="source" value="builtin" />
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
iuc
parents: 0
diff changeset
261 <param name="select_built_in" value="r941_prom_hac_g360+g422" />
63e02ef6e153 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 05505898035b41c07461dc0eecec61699ecbcf41
iuc
parents: 0
diff changeset
262 </conditional>
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iuc
parents: 0
diff changeset
263 <param name="bam_input" value="test1.cram" />
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iuc
parents: 0
diff changeset
264 <conditional name="ref_source">
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iuc
parents: 0
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265 <param name="source" value="history" />
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266 <param name="ref_fasta" value="test1.fasta" />
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267 </conditional>
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268 <output name="merge_output" file="output_cram_test.vcf.gz" ftype="vcf_bgzip"/>
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269 </test>
0
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270 </tests>
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271 <help><![CDATA[
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272 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories:
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273 pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall.
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274 Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.
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275
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276 https://github.com/HKU-BAL/Clair3
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277
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278 LICENSE:
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279
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280 Copyright 2021 The University of Hong Kong, Department of Computer Science
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281
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282 Redistribution and use in source and binary forms, with or without modification,
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283 are permitted provided that the following conditions are met:
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284
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285 1. Redistributions of source code must retain the above copyright notice, this
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286 list of conditions and the following disclaimer.
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287
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288 2. Redistributions in binary form must reproduce the above copyright notice,
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289 this list of conditions and the following disclaimer in the documentation
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290 and/or other materials provided with the distribution.
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291
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292 3. Neither the name of the copyright holder nor the names of its contributors
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293 may be used to endorse or promote products derived from this software without
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294 specific prior written permission.
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295
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296 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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297 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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298 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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299 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
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300 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
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301 (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
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302 LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
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303 ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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304 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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305 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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306 ]]></help>
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307 <citations>
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308 <citation type="doi">10.1101/2021.12.29.474431</citation>
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309 </citations>
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310 </tool>