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comparison clair3.xml @ 1:bd1bbbf7d9b2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c
author iuc
date Tue, 30 Jul 2024 14:23:25 +0000
parents a412acb452ea
children 44914678d18f
comparison
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0:a412acb452ea 1:bd1bbbf7d9b2
1 <tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.09"> 1 <tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
2 <description>germline small variant caller for long-reads</description>
2 <macros> 3 <macros>
3 <token name="@TOOL_VERSION@">0.1.11</token> 4 <token name="@TOOL_VERSION@">1.0.8</token>
4 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
5 </macros> 6 </macros>
7 <xrefs>
8 <xref type='bio.tools'>clair3</xref>
9 </xrefs>
6 <requirements> 10 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">clair3</requirement> 11 <requirement type="package" version="@TOOL_VERSION@">clair3</requirement>
8 </requirements> 12 </requirements>
9 <version_command><![CDATA[run_clair3.sh --version | cut -f2 -d ' ']]></version_command> 13 <version_command><![CDATA[run_clair3.sh --version | cut -f2 -d ' ']]></version_command>
10 <command detect_errors="exit_code"><![CDATA[ 14 <command detect_errors="exit_code"><![CDATA[
16 samtools faidx reference.fasta && 20 samtools faidx reference.fasta &&
17 21
18 #if $model_source.source == "datatable" 22 #if $model_source.source == "datatable"
19 #set model_path = $model_source.model.fields.path 23 #set model_path = $model_source.model.fields.path
20 #end if 24 #end if
21 25 #set $extension = $bam_input.ext
22 ln -s '${$bam_input}' input_reads.bam && 26 ln -s '${$bam_input}' input_reads.$extension &&
23 ln -s '${$bam_input.metadata.bam_index}' input_reads.bai && 27 #if $extension == 'bam'
28 ln -s '${$bam_input.metadata.bam_index}' input_reads.bai &&
29 #else
30 ln -s '${$bam_input.metadata.cram_index}' input_reads.crai &&
31 #end if
24 32
25 #if $bed_or_vcf.bed_or_vcf_selector == 'bed' 33 #if $bed_or_vcf.bed_or_vcf_selector == 'bed'
26 ln -s '$bed_or_vcf.bed_fn' input.bed && 34 ln -s '$bed_or_vcf.bed_fn' input.bed &&
27 #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf' 35 #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf'
28 ln -s '$bed_or_vcf.vcf_fn' input.vcf && 36 ln -s '$bed_or_vcf.vcf_fn' input.vcf &&
29 #end if 37 #end if
30 38
31 run_clair3.sh 39 run_clair3.sh
32 --bam_fn=input_reads.bam 40 --bam_fn=input_reads.$extension
33 --ref_fn=reference.fasta 41 --ref_fn=reference.fasta
34 #if $model_source.source == "datatable" 42 #if $model_source.source == "datatable"
35 --platform='${model_source.model.fields.platform}' 43 --platform='${model_source.model.fields.platform}'
36 --model_path=${model_source.model.fields.path} 44 --model_path=${model_source.model.fields.path}
37 #else 45 #else
41 --platform='ont' 49 --platform='ont'
42 #end if 50 #end if
43 --model_path=\$(dirname \$(which run_clair3.sh))/models/$model_source.select_built_in 51 --model_path=\$(dirname \$(which run_clair3.sh))/models/$model_source.select_built_in
44 #end if 52 #end if
45 --output='.' 53 --output='.'
46 --threads=\${GALAXY_SLOTS:-1} 54 --threads=\${GALAXY_SLOTS:-2}
47 #if $bed_or_vcf.bed_or_vcf_selector == 'bed' 55 #if $bed_or_vcf.bed_or_vcf_selector == 'bed'
48 --bed_fn=input.bed 56 --bed_fn=input.bed
49 #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf' 57 #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf'
50 --vcf_fn=input.vcf 58 --vcf_fn=input.vcf
51 #else 59 #else
52 $bed_or_vcf.include_all_ctgs 60 $bed_or_vcf.include_all_ctgs
53 #end if 61 #end if
54 #if $output_options.selection_mode == 'advanced' 62 $gvcf
55 $output_options.gvcf
56 #end if
57 #if $adv.qual 63 #if $adv.qual
58 --qual=$adv.qual 64 --qual=$adv.qual
59 #end if 65 #end if
60 #if $adv.snp_min_af 66 #if $adv.snp_min_af
61 --snp_min_af=$adv.snp_min_af 67 --snp_min_af=$adv.snp_min_af
68 $adv.print_ref_calls 74 $adv.print_ref_calls
69 $adv.ploidity_model 75 $adv.ploidity_model
70 #if $adv.chunk_size 76 #if $adv.chunk_size
71 --chunk_size=$adv.chunk_size 77 --chunk_size=$adv.chunk_size
72 #end if 78 #end if
73
74 ]]></command> 79 ]]></command>
75 <inputs> 80 <inputs>
81 <param type="data" name="bam_input" argument="--bam_fn" format="bam,cram" label="BAM/CRAM file input" />
76 <conditional name="ref_source"> 82 <conditional name="ref_source">
77 <param type="select" label="Reference genome source" name="source"> 83 <param type="select" label="Reference genome source" name="source">
78 <option value="history" selected="true">History</option> 84 <option value="history" selected="true">History</option>
79 <option value="builtin">Built-in</option> 85 <option value="builtin">Built-in</option>
80 </param> 86 </param>
81 <when value="history"> 87 <when value="history">
82 <param type="data" format="fasta" name="ref_fasta" label="Reference genome" /> 88 <param type="data" format="fasta" name="ref_fasta" argument="--ref_fn" label="Reference genome" />
83 </when> 89 </when>
84 <when value="builtin"> 90 <when value="builtin">
85 <param type="select" name="ref_fasta_builtin" label="Reference genome"> 91 <param type="select" name="ref_fasta_builtin" label="Reference genome">
86 <options from_data_table="all_fasta" /> 92 <options from_data_table="all_fasta" />
87 </param> 93 </param>
88 </when> 94 </when>
89 </conditional> 95 </conditional>
90 <conditional name="model_source"> 96 <conditional name="model_source">
91 <param type="select" label="Select if you want to use built-in models or your own via datatable." name="source"> 97 <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.">
92 <option value="built-in">Built-in</option> 98 <option value="built-in">Built-in</option>
93 <option value="datatable">Datatable</option> 99 <option value="datatable">Cached</option>
94 </param> 100 </param>
95 <when value="built-in"> 101 <when value="built-in">
96 <param type="select" name="select_built_in" label="Select built-in model."> 102 <param type="select" name="select_built_in" label="Built-in model">
97 <option value="r941_prom_sup_g5014">r941_prom_sup_g5014</option> 103 <option value="r941_prom_sup_g5014">r941_prom_sup_g5014</option>
98 <option value="r941_prom_hac_g360+g422">r941_prom_hac_g360+g422</option> 104 <option value="r941_prom_hac_g360+g422">r941_prom_hac_g360+g422</option>
99 <option value="hifi">hifi</option> 105 <option value="hifi">hifi</option>
100 <option value="ilmn">ilmn</option> 106 <option value="ilmn">ilmn</option>
101 </param> 107 </param>
102 </when> 108 </when>
103 <when value="datatable"> 109 <when value="datatable">
104 <param argument="--model_path" type="select" name="model" label="Select model" > 110 <param name="model" argument="--model_path" type="select" label="Cached model from server" >
105 <options from_data_table="clair3_models"> 111 <options from_data_table="clair3_models">
106 <validator type="no_options" message="no modles available" /> 112 <validator type="no_options" message="no cached models available" />
107 </options> 113 </options>
108 </param> 114 </param>
109 </when> 115 </when>
110 </conditional> 116 </conditional>
111 <param type="data" name="bam_input" format="bam" label="BAM file input." /> 117 <conditional name="bed_or_vcf">
112 <conditional name="bed_or_vcf"> 118 <param type="select" name="bed_or_vcf_selector" label="Restrict variant calling to:">
113 <param type="select" name="bed_or_vcf_selector" label="Restict variant calling to:"> 119 <option value="unrestricted" selected="true">Whole reference (unrestricted)</option>
114 <option value="unrestricted" selected="true">Whole reference (unrestricted)</option> 120 <option value="bed" selected="true">Regions defined in BED dataset</option>
115 <option value="bed" selected="true">Regions defined in BED dataset</option> 121 <option value="vcf">Sites defined in VCF dataset</option>
116 <option value="vcf">Sites defined in VCF dataset</option> 122 </param>
117 </param> 123 <when value="bed">
118 <when value="bed"> 124 <param type="data" argument="--bed_fn" format="bed" label="Call variants only in the provided bed regions."/>
119 <param type="data" name="bed_fn" format="bed" label="Call variants only in the provided bed regions."/> 125 </when>
120 </when> 126 <when value="vcf">
121 <when value="vcf"> 127 <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."/>
122 <param type="data" name="vcf_fn" format="vcf" label="Candidate sites VCF file input, variants will only be called at the sites in the VCF file if provided."/> 128 </when>
123 </when> 129 <when value="unrestricted">
124 <when value="unrestricted"> 130 <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}" />
125 <param type="boolean" name="include_all_ctgs" truevalue="--include_all_ctgs" falsevalue="" checked="true" label="Call variants on all contigs, otherwise call in chr{1..22,X,Y} and {1..22,X,Y}, default: disable." /> 131 </when>
126 </when>
127 </conditional>
128 <conditional name="output_options">
129 <param label="Use advanced output options" name="selection_mode" type="select">
130 <option selected="true" value="defaults">Show merged output file only</option>
131 <option value="advanced">Show intermediate output files</option>
132 </param>
133 <when value="defaults"/>
134 <when value="advanced">
135 <param name="full_alignment_check" type="boolean" label="Show full alignment file"/>
136 <param name="pileup_check" type="boolean" label="Show pileup file"/>
137 <param name="phased_bam_check" type="boolean" label="Show itermediate phased BAM file"/>
138 <param type="boolean" name="gvcf" truevalue="--gvcf" falsevalue="" label="Enable GVCF output, default: disable" />
139 </when>
140 </conditional> 132 </conditional>
141 <section name="adv" title="Advanced Parameters" expanded="false"> 133 <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" />
142 <param type="integer" name="qual" value="0" min="0" label="If set, variants with >qual will be marked PASS, or LowQual otherwise." /> 134 <param name="output_files" type="select" display="checkboxes" multiple="true" label="Optional additional output files">
143 <param type="float" name="snp_min_af" value="0.08" min="0" max="1" label="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." /> 135 <option value="full_alignment">Full alignment file</option>
144 <param type="float" name="indel_min_af" value="0.15" min="0" max="1" label="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." /> 136 <option value="pileup">Pileup file</option>
145 <param type="boolean" name="enable_phasing" truevalue="--enable_phasing" falsevalue="" label="Output phased variants using whatshap, default: disable" /> 137 <option value="phased_vcf">Phased VCF file</option>
146 <param type="boolean" name="no_phasing_for_fa" truevalue="--no_phasing_for_fa" falsevalue="" label="EXPERIMENTAL: Call variants without whatshap phasing in full alignment calling, default: disable." /> 138 </param>
147 <param type="boolean" name="print_ref_calls" truevalue="--print_ref_calls" falsevalue="" label="Show reference calls (0/0) in vcf file, default: disable." /> 139 <section name="adv" title="Advanced parameters" expanded="false">
148 <param type="select" name="ploidity_model" label="Call with the following ploidy model" help="EXPERIMENTAL: Enable haploid calling mode. Only 1/1 is considered as a variant, default: disable. EXPERIMENTAL: Enable haploid calling mode. 0/1 and 1/1 are considered as a variant, default: disable."> 140 <param type="integer" argument="--qual" value="0" min="0" label="Qual" help="If set, variants with >qual will be marked PASS, or LowQual otherwise." />
149 <option value="" selected="true">diploid</option> 141 <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." />
150 <option value="--haploid_sensitive">haploid (sensitive)</option> 142 <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." />
151 <option value="--haploid_precise">haploid (precise)</option> 143 <param type="boolean" argument="--enable_phasing" truevalue="--enable_phasing" falsevalue="" label="Enable phasing" help="Output phased variants using whatshap. Default: disable" />
144 <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" />
145 <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." />
146 <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.">
147 <option value="" selected="true">Diploid</option>
148 <option value="--haploid_sensitive">Haploid sensitive (--haploid_sensitive)</option>
149 <option value="--haploid_precise">haploid precise (--haploid_precise)</option>
152 </param> 150 </param>
153 <param type="integer" name="chunk_size" value="5000000" min="1" label="The size of each chuck for parallel processing, default: 5Mbp." optional="true" /> 151 <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" />
154 </section> 152 </section>
155 </inputs> 153 </inputs>
156 <outputs> 154 <outputs>
157 <data name="merge_output" format="vcf_bgzip" from_work_dir="./merge_output.vcf.gz" /> 155 <data name="merge_output" format="vcf_bgzip" from_work_dir="./merge_output.vcf.gz" label="${tool.name} on ${on_string}: merged output"/>
158 <data name="pileup" format="vcf_bgzip" from_work_dir="./pileup.vcf.gz"> 156 <data name="pileup" format="vcf_bgzip" from_work_dir="./pileup.vcf.gz" label="${tool.name} on ${on_string}: pileup">
159 <filter>output_options['selection_mode'] == 'advanced' and output_options['pileup_check']</filter> 157 <filter>output_files and 'pileup' in output_files</filter>
160 </data> 158 </data>
161 <data name="full_alignment" format="vcf_bgzip" from_work_dir="./full_alignment.vcf.gz"> 159 <data name="full_alignment" format="vcf_bgzip" from_work_dir="./full_alignment.vcf.gz" label="${tool.name} on ${on_string}: full alignment">
162 <filter>output_options['selection_mode'] == 'advanced' and output_options['full_alignment_check']</filter> 160 <filter>output_files and 'full_alignment' in output_files</filter>
163 </data> 161 </data>
164 <data name="phased_bam" format="bam" from_work_dir="./phased_bam.bam"> 162 <data name="phased_vcf" format="vcf_bgzip" from_work_dir="./phased_merge_output.vcf.gz" label="${tool.name} on ${on_string}: phased VCF">
165 <filter>output_options['selection_mode'] == 'advanced' and output_options['phased_bam_check']</filter> 163 <filter>output_files and 'phased_vcf' in output_files</filter>
166 </data> 164 </data>
167 </outputs> 165 </outputs>
168 <tests> 166 <tests>
167 <!-- test1 -->
169 <test expect_num_outputs="1"> 168 <test expect_num_outputs="1">
170 <conditional name="model_source"> 169 <conditional name="model_source">
171 <param name="source" value="built-in"/> 170 <param name="source" value="built-in"/>
172 <param name="select_built_in" value="r941_prom_hac_g360+g422"/> 171 <param name="select_built_in" value="r941_prom_hac_g360+g422"/>
173 </conditional> 172 </conditional>
177 <param name="ref_fasta" value="test1.fasta" /> 176 <param name="ref_fasta" value="test1.fasta" />
178 </conditional> 177 </conditional>
179 <conditional name="bed_or_vcf"> 178 <conditional name="bed_or_vcf">
180 <param name="bed_or_vcf_selector" value="vcf"/> 179 <param name="bed_or_vcf_selector" value="vcf"/>
181 <param name="vcf_fn" value="test1.vcf.gz" /> 180 <param name="vcf_fn" value="test1.vcf.gz" />
182 </conditional>
183 <conditional name="output_options">
184 <param name="selection_mode" value="advanced"/>
185 <param name="gvcf" value="true" />
186 </conditional> 181 </conditional>
187 <section name="adv"> 182 <section name="adv">
188 <param name="no_phasing_for_fa" value="true"/> 183 <param name="no_phasing_for_fa" value="true"/>
189 <param name="print_ref_calls" value="true"/> 184 <param name="print_ref_calls" value="true"/>
190 <param name="ploidity_model" value=""/> 185 <param name="ploidity_model" value=""/>
191 </section> 186 </section>
192 <assert_stdout> 187 <assert_stdout>
193 <has_text text="[WARNING] No contig intersection found, output header only in" /> 188 <has_text text="[WARNING] No contig intersection found, output header only in" />
194 </assert_stdout> 189 </assert_stdout>
195 </test> 190 </test>
191 <!-- test2 -->
196 <test expect_num_outputs="4"> 192 <test expect_num_outputs="4">
197 <conditional name="model_source"> 193 <conditional name="model_source">
198 <param name="source" value="builtin" /> 194 <param name="source" value="built-in" />
199 <param name="select_built_in" value="r941_prom_hac_g360+g422" /> 195 <param name="select_built_in" value="r941_prom_hac_g360+g422" />
200 </conditional> 196 </conditional>
201 <param name="bam_input" value="test1.bam" /> 197 <param name="bam_input" value="test1.bam" />
202 <conditional name="bed_or_vcf"> 198 <conditional name="bed_or_vcf">
203 <param name="bed_or_vcf_selector" value="unrestricted"/> 199 <param name="bed_or_vcf_selector" value="unrestricted"/>
205 </conditional> 201 </conditional>
206 <conditional name="ref_source"> 202 <conditional name="ref_source">
207 <param name="source" value="builtin" /> 203 <param name="source" value="builtin" />
208 <param name="ref_fasta_builtin" value="test1" /> 204 <param name="ref_fasta_builtin" value="test1" />
209 </conditional> 205 </conditional>
210 <conditional name="output_options"> 206 <param name="gvcf" value="true"/>
211 <param name="selection_mode" value="advanced"/> 207 <param name="output_files" value="full_alignment,pileup,phased_vcf"/>
212 <param name="pileup_check" value="true"/>
213 <param name="full_alignment_check" value="true"/>
214 <param name="phased_bam_check" value="true"/>
215 </conditional>
216 <section name="adv"> 208 <section name="adv">
217 <param name="print_ref_calls" value="true"/> 209 <param name="print_ref_calls" value="true"/>
210 <param name="enable_phasing" value="true"/>
218 </section> 211 </section>
219 <output name="merge_output" decompress="true" file="merge_output_1.vcf" ftype="vcf_bgzip"/> 212 <output name="merge_output" decompress="true" file="merge_output_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
220 <output name="pileup" decompress="true" file="pileup_1.vcf" ftype="vcf_bgzip"/> 213 <output name="pileup" decompress="true" file="pileup_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
221 <output name="full_alignment" decompress="true" file="full_alignment_1.vcf" ftype="vcf_bgzip"/> 214 <output name="full_alignment" decompress="true" file="full_alignment_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
222 <output name="phased_bam" file="phased_bam_1.bam" ftype="bam"/> 215 <output name="phased_vcf" decompress="true" file="phased_vcf_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
223 </test> 216 </test>
217 <!-- test3 -->
224 <test expect_num_outputs="4"> 218 <test expect_num_outputs="4">
225 <conditional name="model_source"> 219 <conditional name="model_source">
226 <param name="source" value="datatable" /> 220 <param name="source" value="datatable" />
227 <param name="model" value="test_model" /> 221 <param name="model" value="test_model" />
228 </conditional> 222 </conditional>
233 </conditional> 227 </conditional>
234 <conditional name="ref_source"> 228 <conditional name="ref_source">
235 <param name="source" value="builtin" /> 229 <param name="source" value="builtin" />
236 <param name="ref_fasta_builtin" value="test1" /> 230 <param name="ref_fasta_builtin" value="test1" />
237 </conditional> 231 </conditional>
238 <conditional name="output_options"> 232 <param name="output_files" value="full_alignment,pileup,phased_vcf"/>
239 <param name="selection_mode" value="advanced"/>
240 <param name="pileup_check" value="true"/>
241 <param name="full_alignment_check" value="true"/>
242 <param name="phased_bam_check" value="true"/>
243 </conditional>
244 <section name="adv"> 233 <section name="adv">
245 <param name="snp_min_af" value="0.5"/> 234 <param name="snp_min_af" value="0.5"/>
246 <param name="indel_min_af" value="0.12"/> 235 <param name="indel_min_af" value="0.12"/>
247 <param name="no_phasing_for_fa" value="true" /> 236 <param name="no_phasing_for_fa" value="true" />
248 <param name="print_ref_calls" value="true"/> 237 <param name="print_ref_calls" value="true"/>
249 </section> 238 </section>
250 <output name="merge_output" ftype="vcf_bgzip"> 239 <output name="merge_output" decompress="true" ftype="vcf_bgzip">
251 <assert_contents> 240 <assert_contents>
252 <has_size value="450" delta="50" /> 241 <has_text text="#CHROM" />
253 </assert_contents> 242 </assert_contents>
254 </output> 243 </output>
255 <output name="pileup" ftype="vcf_bgzip"> 244 <output name="pileup" ftype="vcf_bgzip">
256 <assert_contents> 245 <assert_contents>
257 <has_size value="0" /> 246 <has_size value="0" />
260 <output name="full_alignment" ftype="vcf_bgzip"> 249 <output name="full_alignment" ftype="vcf_bgzip">
261 <assert_contents> 250 <assert_contents>
262 <has_size value="0" /> 251 <has_size value="0" />
263 </assert_contents> 252 </assert_contents>
264 </output> 253 </output>
265 <output name="phased_bam" ftype="bam"> 254 <output name="phased_vcf" ftype="vcf_bgzip">
266 <assert_contents> 255 <assert_contents>
267 <has_size value="0" /> 256 <has_size value="0" />
268 </assert_contents> 257 </assert_contents>
269 </output> 258 </output>
259 </test>
260 <!-- test4 -->
261 <!-- Test input CRAM -->
262 <test expect_num_outputs="1">
263 <conditional name="model_source">
264 <param name="source" value="built-in" />
265 <param name="select_built_in" value="r941_prom_hac_g360+g422" />
266 </conditional>
267 <param name="bam_input" value="test1.cram" />
268 <conditional name="ref_source">
269 <param name="source" value="history" />
270 <param name="ref_fasta" value="test1.fasta" />
271 </conditional>
272 <output name="merge_output" decompress="true" file="output_cram_test.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
270 </test> 273 </test>
271 </tests> 274 </tests>
272 <help><![CDATA[ 275 <help><![CDATA[
273 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: 276 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories:
274 pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. 277 pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall.