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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit 908fb9148a3a116dbf7ccd16e0992e7882e748c2
author iuc
date Tue, 30 Apr 2024 08:38:15 +0000
parents 271eb7f4b8bc
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1:271eb7f4b8bc 2:800f8086da7d
1 <tool id="hapcut2" name="Hapcut2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@+ga@GA_VERSION_SUFFIX@"> 1 <tool id="hapcut2" name="Hapcut2" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
2 <description> - haplotype assembly for diploid organisms</description> 2 <description>haplotype assembly for diploid organisms</description>
3 <macros>
4 <token name="@TOOL_VERSION@">1.3.4</token>
5 <token name="@VERSION_SUFFIX@">1</token>
6 <import>macros.xml</import>
7 </macros>
3 <xrefs> 8 <xrefs>
4 <xref type="bio.tools">hapcut2</xref> 9 <xref type="bio.tools">hapcut2</xref>
5 </xrefs> 10 </xrefs>
6 <macros>
7 <token name="@TOOL_VERSION@">1.3.3</token>
8 <token name="@VERSION_SUFFIX@">0</token>
9 <token name="@GA_VERSION_SUFFIX@">1</token>
10 </macros>
11 <requirements> 11 <requirements>
12 <requirement type="package" version="1.3.3">hapcut2</requirement> 12 <requirement type="package" version="@TOOL_VERSION@">hapcut2</requirement>
13 </requirements> 13 </requirements>
14
15 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
16 15
17 ## Prep inputs 16 ## Prep inputs
18 ## ===================================================================== 17 ## =====================================================================
19 ln -s '$input_bam' input.bam 18 ln -s '$input_bam' input.bam
20 && ln -s '$input_vcf' input.vcf 19 && ln -s '$input_vcf' input.vcf
21 20
21 ## Set reference genome if required
22 #if $optimization.choice in ['pacbio', 'ont']:
23 #if $optimization.reference_genome.source == 'index':
24 #set $ref_genome_path = $optimization.reference_genome.index.fields.path
25 #else
26 #set $ref_genome_path = $optimization.reference_genome.fasta
27 #end if
28 #end if
22 29
23 ## Run program 30 ## Run program
24 ## ===================================================================== 31 ## =====================================================================
25 ## Extract variant fragments from alignment 32 ## Extract variant fragments from alignment
26 && extractHAIRS --bam input.bam --VCF input.vcf --out frags.dat 33 && extractHAIRS --bam 'input.bam' --VCF 'input.vcf' --out frags.dat
27 #if $optimization.choice == 'pacbio': 34 #if $optimization.choice == 'pacbio':
28 --pacbio 1 35 --pacbio 1
29 --ref '$optimization.reference_fasta' 36 --ref '$ref_genome_path'
30 #elif $optimization.choice == 'ont': 37 #elif $optimization.choice == 'ont':
31 --ont 1 38 --ont 1
32 --ref '$optimization.reference_fasta' 39 --ref '$ref_genome_path'
33 #elif $optimization.choice == 'hic': 40 #elif $optimization.choice == 'hic':
34 --HiC 1 41 --HiC 1
35 #end if 42 #end if
36 43
37 #if $advanced.minIS 44 #if $advanced.minIS
38 --minIS $advanced.minIS 45 --minIS $advanced.minIS
39 #end if 46 #end if
40 47
41 #if $advanced.maxIS 48 #if $advanced.maxIS
42 --maxIS $advanced.maxIS 49 --maxIS $advanced.maxIS
43 #end if 50 #end if
45 ## Create haplotype.out and haplotype.out.phased.VCF 52 ## Create haplotype.out and haplotype.out.phased.VCF
46 && HAPCUT2 --fragments frags.dat --VCF input.vcf --output haplotype.out 53 && HAPCUT2 --fragments frags.dat --VCF input.vcf --output haplotype.out
47 #if $optimization.choice == 'hic': 54 #if $optimization.choice == 'hic':
48 --HiC 1 55 --HiC 1
49 #end if 56 #end if
50
51 ]]></command> 57 ]]></command>
52 58
53 <inputs> 59 <inputs>
54 <param name="input_bam" type="data" format="bam" label="Input BAM file"/> 60 <param name="input_bam" argument="--bam" type="data" format="bam" label="Input BAM file" help="Coordinate-sorted BAM file"/>
55 <param name="input_vcf" type="data" format="vcf" label="Input VCF file"/> 61 <param name="input_vcf" argument="--VCF" type="data" format="vcf" label="Input VCF file" help="Variant file with genotypes for a single individual"/>
56
57 <conditional name="optimization"> 62 <conditional name="optimization">
58 <!-- TODO: include 10X (requires extra processing step) --> 63 <!-- TODO: include 10X (requires extra processing step) -->
59 <param name="choice" type="select" display="radio" label="Optimization"> 64 <param name="choice" type="select" display="radio" label="Optimization">
60 <option value="default" selected="true">Default</option> 65 <option value="default" selected="true">Default</option>
61 <option value="pacbio">Pacbio</option> 66 <option value="pacbio">Pacbio</option>
62 <option value="ont">Oxford Nanopore</option> 67 <option value="ont">Oxford Nanopore</option>
63 <option value="hic">Hi-C</option> 68 <option value="hic">Hi-C</option>
64 </param> 69 </param>
65 70 <when value="default"></when>
66 <when value="pacbio"> 71 <when value="pacbio">
67 <param name="reference_fasta" type="data" format="fasta" 72 <expand macro="reference_genome_input"/>
68 label="Reference genome fasta file"
69 help="The reference genome is required for long-read optimization."
70 />
71 </when> 73 </when>
72
73 <when value="ont"> 74 <when value="ont">
74 <param name="reference_fasta" type="data" format="fasta" 75 <expand macro="reference_genome_input"/>
75 label="Reference genome fasta file"
76 help="The reference genome is required for long-read optimization."
77 />
78 </when> 76 </when>
77 <when value="hic"></when>
79 </conditional> 78 </conditional>
80 79
81 <param name="output_phased" type="boolean" label="Output phased VCF file?" 80 <param name="output_phased" type="boolean" label="Output phased VCF file?" checked="true" help="Output variant calls on the haplotype assembly"/>
82 checked="true" 81 <param name="output_fragments" type="boolean" label="Output fragments file?" help="Output fragments collected by extractHAIRS"/>
83 help="Output variant calls on the haplotype assembly"
84 />
85 <param name="output_fragments" type="boolean" label="Output fragments file?"
86 help="Output fragments collected by extractHAIRS"
87 />
88
89 82
90 <section name="advanced" title="Advanced parameters"> 83 <section name="advanced" title="Advanced parameters">
91 <param name="maxIS" type="integer" label="Maximum insert size" 84 <param argument="--maxIS" type="integer" label="Maximum insert size" optional="true" value="1000" min="0" help="Maximum insert size for a paired-end read to be considered as a single fragment for phasing"/>
92 optional="true" value="1000" 85 <param argument="--minIS" type="integer" label="Minimum insert size" optional="true" value="0" min="0" help="Minimum insert size for a paired-end read to be considered as a single fragment for phasing"/>
93 help="Maximum insert size for a paired-end read to be considered as a single fragment for phasing."
94 />
95
96 <param name="minIS" type="integer" label="Minimum insert size"
97 optional="true" value="0"
98 help="Minimum insert size for a paired-end read to be considered as a single fragment for phasing."
99 />
100 </section> 86 </section>
101 </inputs> 87 </inputs>
102 88
103 <outputs> 89 <outputs>
104 <data name="haplotype" format="txt" from_work_dir="haplotype.out" 90 <data name="haplotype" format="txt" from_work_dir="haplotype.out" label="${tool.name} on ${on_string}: Haplotype block"/>
105 label="${tool.name} on ${on_string}: Haplotype block" 91 <data name="haplotype_phased" format="vcf" from_work_dir="haplotype.out.phased.VCF" label="${tool.name} on ${on_string}: Phased haplotype VCF">
106 />
107 <data name="haplotype_phased" format="vcf" from_work_dir="haplotype.out.phased.VCF"
108 label="${tool.name} on ${on_string}: Phased haplotype VCF"
109 >
110 <filter>output_phased</filter> 92 <filter>output_phased</filter>
111 </data> 93 </data>
112 <data name="frags" format="txt" from_work_dir="frags.dat" 94 <data name="frags" format="txt" from_work_dir="frags.dat" label="${tool.name} on ${on_string}: Fragments">
113 label="${tool.name} on ${on_string}: Fragments"
114 >
115 <filter>output_fragments</filter> 95 <filter>output_fragments</filter>
116 </data> 96 </data>
117 </outputs> 97 </outputs>
118 98
119 <tests> 99 <tests>
120 <test expect_num_outputs="3"> 100 <!-- Defaults -->
121 <param name="input_bam" ftype="bam" value="input.bam"/> 101 <test expect_num_outputs="1">
122 <param name="input_vcf" ftype="vcf" value="input.vcf"/> 102 <param name="input_bam" ftype="bam" value="input.bam"/>
123 <param name="output_fragments" value="1"/> 103 <param name="input_vcf" ftype="vcf" value="input.vcf"/>
124 <param name="output_phased" value="1"/> 104 <param name="output_fragments" value="0"/>
125 <param name="optimization" value="default"/> 105 <param name="output_phased" value="0"/>
126 <output name="frags" ftype="txt" file="output_frag.dat"/> 106 <conditional name="optimization">
127 <output name="haplotype" ftype="txt" file="output_haplotype.out"/> 107 <param name="choice" value="default"/>
128 <output name="haplotype_phased" ftype="vcf" file="output_haplotype.out.phased.vcf"/> 108 </conditional>
109 <output name="haplotype" ftype="txt" file="output_haplotype.out"/>
110 </test>
111
112 <!-- Defaults with all outputs -->
113 <test expect_num_outputs="3">
114 <param name="input_bam" ftype="bam" value="input.bam"/>
115 <param name="input_vcf" ftype="vcf" value="input.vcf"/>
116 <param name="output_fragments" value="1"/>
117 <param name="output_phased" value="1"/>
118 <conditional name="optimization">
119 <param name="choice" value="default"/>
120 </conditional>
121 <output name="frags" ftype="txt" file="output_frag.dat"/>
122 <output name="haplotype" ftype="txt" file="output_haplotype.out"/>
123 <output name="haplotype_phased" ftype="vcf" file="output_haplotype.out.phased.vcf"/>
124 </test>
125
126 <!-- Hi-C optimization -->
127 <test expect_num_outputs="3">
128 <param name="input_bam" ftype="bam" value="input.bam"/>
129 <param name="input_vcf" ftype="vcf" value="input.vcf"/>
130 <param name="output_fragments" value="1"/>
131 <param name="output_phased" value="1"/>
132 <conditional name="optimization">
133 <param name="choice" value="default"/>
134 </conditional>
135 <output name="frags" ftype="txt" file="output_frag.dat"/>
136 <output name="haplotype" ftype="txt" file="output_haplotype.out"/>
137 <output name="haplotype_phased" ftype="vcf" file="output_haplotype.out.phased.vcf"/>
138 </test>
139
140 <!-- Pacbio optimization with ref genome -->
141 <test expect_num_outputs="3">
142 <param name="input_bam" ftype="bam" value="input.bam"/>
143 <param name="input_vcf" ftype="vcf" value="input.vcf"/>
144 <param name="output_fragments" value="1"/>
145 <param name="output_phased" value="1"/>
146 <conditional name="optimization">
147 <param name="choice" value="pacbio"/>
148 </conditional>
149 <conditional name="reference_genome">
150 <param name="source" value="history"/>
151 </conditional>
152 <param name="fasta" ftype="fasta" value="ref.fasta"/>
153 <output name="frags" ftype="txt" file="output_frag.dat"/>
154 <output name="haplotype" ftype="txt" file="output_haplotype.out"/>
155 <output name="haplotype_phased" ftype="vcf" file="output_haplotype.out.phased.vcf"/>
156 </test>
157
158 <!-- Oxford nanopore optimization with ref genome -->
159 <test expect_num_outputs="3">
160 <param name="input_bam" ftype="bam" value="input.bam"/>
161 <param name="input_vcf" ftype="vcf" value="input.vcf"/>
162 <param name="output_fragments" value="1"/>
163 <param name="output_phased" value="1"/>
164 <output name="frags" ftype="txt" file="output_frag.dat"/>
165 <output name="haplotype" ftype="txt" file="output_haplotype.out"/>
166 <output name="haplotype_phased" ftype="vcf" file="output_haplotype.out.phased.vcf"/>
167 <conditional name="optimization">
168 <param name="optimization" value="ont"/>
169 </conditional>
170 <conditional name="reference_genome">
171 <param name="source" value="history"/>
172 </conditional>
173 <param name="fasta" ftype="fasta" value="ref.fasta"/>
129 </test> 174 </test>
130 </tests> 175 </tests>
131 176
132 <help><![CDATA[ 177 <help><![CDATA[
133 .. class:: infomark 178 .. class:: infomark
170 215
171 See `HapCUT2 on GitHib <https://github.com/vibansal/HapCUT2>`_ for more detailed information. 216 See `HapCUT2 on GitHib <https://github.com/vibansal/HapCUT2>`_ for more detailed information.
172 217
173 ]]></help> 218 ]]></help>
174 <citations> 219 <citations>
175 <citation type="doi">https://doi.org/10.1101/gr.213462.116</citation> 220 <citation type="doi">10.1101/gr.213462.116</citation>
176 </citations> 221 </citations>
222 <expand macro="creator"/>
177 </tool> 223 </tool>