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annotate hap.py.xml @ 2:9c358e648d74 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
author iuc
date Fri, 24 Oct 2025 13:26:46 +0000
parents 37c4cd0fdfc5
children
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9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
iuc
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1 <tool id="som.py" name="som.py and hap.py" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
iuc
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2 <description>Comparison of somatic callsets based only on chromosome, position, and allele identity</description>
0
37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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3 <macros>
2
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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4 <token name="@TOOL_VERSION@">0.3.15</token>
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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5 <token name="@PROFILE@">24.1</token>
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6 <token name="@VERSION_SUFFIX@">0</token>
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7 </macros>
2
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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8 <xrefs>
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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9 <xref type="bio.tools">hap.py</xref>
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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10 </xrefs>
0
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11 <requirements>
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12 <requirement type="package" version="@TOOL_VERSION@">hap.py</requirement>
37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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13 </requirements>
2
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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14 <version_command>som.py -h</version_command>
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37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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15 <command detect_errors="exit_code"><![CDATA[
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16 #if $reference_genome.source == 'history':
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17 #set $ref_genome = 'reference.fasta'
37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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18 ln -s -f '${reference_genome.history_item}' $ref_genome;
37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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19 samtools faidx $ref_genome;
37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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20 #else:
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21 #set $ref_genome = $reference_genome.index.fields.path
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22 #end if
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23 export HGREF='$ref_genome' &&
2
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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24 #if $program_select == 'som.py':
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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25 som.py
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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26 #else:
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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27 hap.py
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28 #end if
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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29 '$truth'
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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30 '$query'
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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31 -r '$ref_genome'
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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32 -o output
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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33 | sed 's/\s\+/\t/g' | tail -n+2 > results.tsv
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37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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34 ]]>
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35 </command>
37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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36 <inputs>
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37 <param name="program_select" type="select" label="Comparison method" help="Select the comparison method to use.">
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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38 <option value="som.py">som.py: Genotype-level comparison</option>
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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39 <option value="hap.py">hap.py: Allele-based comparison (chromosome, position, allele)</option>
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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40 </param>
0
37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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41 <conditional name="reference_genome">
37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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42 <param name="source" type="select" label="Source for the reference genome" help="Built-in references were created using default options.">
37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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43 <option value="indexed" selected="true">Use a built-in genome</option>
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44 <option value="history">Use a genome from history</option>
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45 </param>
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46 <when value="indexed">
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47 <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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48 <options from_data_table="fasta_indexes">
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49 <filter type="sort_by" column="2"/>
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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50 <validator type="no_options" message="No genomes are available for the selected input dataset"/>
0
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51 </options>
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52 </param>
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53 </when>
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54 <when value="history">
2
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55 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format"/>
0
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56 </when>
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57 </conditional>
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58 <param name="truth" type="data" format="vcf" label="ground truth variant calls"/>
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59 <param name="query" type="data" format="vcf" label="query variant calls"/>
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60 </inputs>
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61 <outputs>
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62 <data name="results" label="${tool.name} on ${on_string}" format="tabular" from_work_dir="results.tsv"/>
2
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63 <data name="sompy_metrics" label="${tool.name} on ${on_string}: som.py metrics" format="json" from_work_dir="output.metrics.json">
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64 <filter>'som.py' in program_select </filter>
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65 </data>
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66 <data name="happy_metrics" label="${tool.name} on ${on_string}: hap.py metrics" format="json" from_work_dir="output.metrics.json.gz">
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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67 <filter>'hap.py' in program_select </filter>
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68 </data>
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69 <data name="stats" label="${tool.name} on ${on_string}: som.py comparison stats" format="csv" from_work_dir="output.stats.csv">
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70 <filter>'som.py' in program_select </filter>
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71 </data>
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72 <data name="summary" label="${tool.name} on ${on_string}: hap.py summary" format="csv" from_work_dir="output.summary.csv">
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73 <filter>'hap.py' in program_select </filter>
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74 </data>
0
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75 </outputs>
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76 <tests>
2
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77 <!-- Testing som.py -->
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78 <test expect_num_outputs="3">
2
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79 <param name="program_select" value="som.py"/>
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80 <conditional name="reference_genome">
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81 <param name="source" value="history"/>
9c358e648d74 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy commit 4abfaf634dcfed1dfce1bcf199c12acc33982ba4
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82 <param name="history_item" value="chr21.fa"/>
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83 </conditional>
0
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84 <param name="truth" value="small_NA12878-Freebayes-chr21.vcf"/>
37c4cd0fdfc5 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/happy commit 9ae0037c379b589aa8e0f825820bb4a7c969cdb2"
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85 <param name="query" value="small_NA12878-GATK3-chr21.vcf"/>
2
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86 <output name="results">
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87 <assert_contents>
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88 <has_text text="records"/>
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89 <has_n_lines n="4"/>
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90 </assert_contents>
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91 </output>
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92 <output name="stats">
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93 <assert_contents>
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94 <has_line_matching expression="^0,indels,1,1,0,1.*"/>
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95 <has_text text="som.py-"/>
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96 </assert_contents>
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97 </output>
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98 <output name="sompy_metrics">
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99 <assert_contents>
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100 <has_json_property_with_text property="name" text="som.py.comparison"/>
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101 <has_text text="som.py.comparison"/>
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102 </assert_contents>
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103 </output>
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104 </test>
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105 <!-- Testing hap.py -->
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106 <test expect_num_outputs="3">
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107 <param name="program_select" value="hap.py"/>
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108 <conditional name="reference_genome">
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109 <param name="source" value="history"/>
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110 <param name="history_item" value="reference.fasta"/>
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111 </conditional>
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112 <param name="truth" value="hap_py_truth.vcf.gz"/>
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113 <param name="query" value="hap_py_query.vcf.gz"/>
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114 <output name="results">
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115 <assert_contents>
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116 <has_n_lines n="6"/>
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117 </assert_contents>
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118 </output>
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119 <output name="summary">
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120 <assert_contents>
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121 <has_n_lines n="5"/>
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122 <has_text text="SNP,PASS,5,4,1,6,2,0,0,0,0.8,0.666667,0.0,0.727273,0.25,0.5,0.0,0.0"/>
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123 </assert_contents>
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124 </output>
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125 <output name="happy_metrics" decompress="true">
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126 <assert_contents>
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127 <has_json_property_with_text property="name" text="hap.py.comparison"/>
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128 <has_text text="hap.py.comparison"/>
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129 </assert_contents>
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130 </output>
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131 </test>
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132 </tests>
2
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133 <help format="markdown"><![CDATA[
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134
2
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135 ## What this tool does
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136 **hap.py** compares variant callsets (VCFs) against a reference “truth” set to evaluate variant calling accuracy. It performs haplotype-aware comparisons, matching variants by local sequence context rather than simple record alignment. This enables accurate benchmarking even when complex or multi-nucleotide variants are represented differently.
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137 ---
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138
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139 ## Inputs
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140 - **Truth VCF:** High-confidence reference variants.
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141 - **Query VCF:** Variants to evaluate.
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142 - **Reference FASTA:** Genome reference used for both callsets.
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143 ---
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144
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145 ## Outputs
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146 - **Summary CSV / JSON:** Precision, recall, and F1 metrics.
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147 - **ROC and stratified metrics:** Optional, for detailed performance breakdowns.
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148 - **Annotated VCFs:** Optional lists of matched and unmatched variants.
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149 ---
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150
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151 ## Notes
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152 - Use **hap.py** for haplotype-level benchmarking.
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153 - Use **som.py** for simpler allele-based comparisons (chromosome, position, allele).
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154 ]]></help>
2
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155 <citations>
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156 <citation type="bibtex">@misc{illumina_happy,
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157 title = {hap.py},
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158 author = {{Illumina}},
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159 year = {2021},
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160 howpublished = {\url{https://github.com/Illumina/hap.py}},
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161 note = {Accessed: 2025-10-19}
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162 }</citation>
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163 </citations>
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164 </tool>