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comparison clair3.xml @ 2:c8ba8286e7c0 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 14:23:36 +0000
parents 63e02ef6e153
children 3843a30053ee
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1:63e02ef6e153 2:c8ba8286e7c0
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 <description>germline small variant caller for long-reads</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">0.1.12</token> 4 <token name="@TOOL_VERSION@">1.0.8</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">0</token>
6 </macros> 6 </macros>
7 <xrefs> 7 <xrefs>
8 <xref type='bio.tools'>clair3</xref> 8 <xref type='bio.tools'>clair3</xref>
9 </xrefs> 9 </xrefs>
74 $adv.print_ref_calls 74 $adv.print_ref_calls
75 $adv.ploidity_model 75 $adv.ploidity_model
76 #if $adv.chunk_size 76 #if $adv.chunk_size
77 --chunk_size=$adv.chunk_size 77 --chunk_size=$adv.chunk_size
78 #end if 78 #end if
79
80 ]]></command> 79 ]]></command>
81 <inputs> 80 <inputs>
82 <param type="data" name="bam_input" argument="--bam_fn" format="bam,cram" label="BAM/CRAM file input" /> 81 <param type="data" name="bam_input" argument="--bam_fn" format="bam,cram" label="BAM/CRAM file input" />
83 <conditional name="ref_source"> 82 <conditional name="ref_source">
84 <param type="select" label="Reference genome source" name="source"> 83 <param type="select" label="Reference genome source" name="source">
114 </options> 113 </options>
115 </param> 114 </param>
116 </when> 115 </when>
117 </conditional> 116 </conditional>
118 <conditional name="bed_or_vcf"> 117 <conditional name="bed_or_vcf">
119 <param type="select" name="bed_or_vcf_selector" label="Restict variant calling to:"> 118 <param type="select" name="bed_or_vcf_selector" label="Restrict variant calling to:">
120 <option value="unrestricted" selected="true">Whole reference (unrestricted)</option> 119 <option value="unrestricted" selected="true">Whole reference (unrestricted)</option>
121 <option value="bed" selected="true">Regions defined in BED dataset</option> 120 <option value="bed" selected="true">Regions defined in BED dataset</option>
122 <option value="vcf">Sites defined in VCF dataset</option> 121 <option value="vcf">Sites defined in VCF dataset</option>
123 </param> 122 </param>
124 <when value="bed"> 123 <when value="bed">
133 </conditional> 132 </conditional>
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" /> 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" />
135 <param name="output_files" type="select" display="checkboxes" multiple="true" label="Optional additional output files"> 134 <param name="output_files" type="select" display="checkboxes" multiple="true" label="Optional additional output files">
136 <option value="full_alignment">Full alignment file</option> 135 <option value="full_alignment">Full alignment file</option>
137 <option value="pileup">Pileup file</option> 136 <option value="pileup">Pileup file</option>
138 <option value="phased_bam">Phased BAM file</option> 137 <option value="phased_vcf">Phased VCF file</option>
139 </param> 138 </param>
140 <section name="adv" title="Advanced parameters" expanded="false"> 139 <section name="adv" title="Advanced parameters" expanded="false">
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." /> 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." />
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." /> 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." />
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." /> 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." />
158 <filter>output_files and 'pileup' in output_files</filter> 157 <filter>output_files and 'pileup' in output_files</filter>
159 </data> 158 </data>
160 <data name="full_alignment" format="vcf_bgzip" from_work_dir="./full_alignment.vcf.gz" label="${tool.name} on ${on_string}: full alignment"> 159 <data name="full_alignment" format="vcf_bgzip" from_work_dir="./full_alignment.vcf.gz" label="${tool.name} on ${on_string}: full alignment">
161 <filter>output_files and 'full_alignment' in output_files</filter> 160 <filter>output_files and 'full_alignment' in output_files</filter>
162 </data> 161 </data>
163 <data name="phased_bam" format="bam" from_work_dir="./phased_bam.bam" label="${tool.name} on ${on_string}: phased BAM"> 162 <data name="phased_vcf" format="vcf_bgzip" from_work_dir="./phased_merge_output.vcf.gz" label="${tool.name} on ${on_string}: phased VCF">
164 <filter>output_files and 'phased_bam' in output_files</filter> 163 <filter>output_files and 'phased_vcf' in output_files</filter>
165 </data> 164 </data>
166 </outputs> 165 </outputs>
167 <tests> 166 <tests>
167 <!-- test1 -->
168 <test expect_num_outputs="1"> 168 <test expect_num_outputs="1">
169 <conditional name="model_source"> 169 <conditional name="model_source">
170 <param name="source" value="built-in"/> 170 <param name="source" value="built-in"/>
171 <param name="select_built_in" value="r941_prom_hac_g360+g422"/> 171 <param name="select_built_in" value="r941_prom_hac_g360+g422"/>
172 </conditional> 172 </conditional>
186 </section> 186 </section>
187 <assert_stdout> 187 <assert_stdout>
188 <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" />
189 </assert_stdout> 189 </assert_stdout>
190 </test> 190 </test>
191 <!-- test2 -->
191 <test expect_num_outputs="4"> 192 <test expect_num_outputs="4">
192 <conditional name="model_source"> 193 <conditional name="model_source">
193 <param name="source" value="builtin" /> 194 <param name="source" value="built-in" />
194 <param name="select_built_in" value="r941_prom_hac_g360+g422" /> 195 <param name="select_built_in" value="r941_prom_hac_g360+g422" />
195 </conditional> 196 </conditional>
196 <param name="bam_input" value="test1.bam" /> 197 <param name="bam_input" value="test1.bam" />
197 <conditional name="bed_or_vcf"> 198 <conditional name="bed_or_vcf">
198 <param name="bed_or_vcf_selector" value="unrestricted"/> 199 <param name="bed_or_vcf_selector" value="unrestricted"/>
201 <conditional name="ref_source"> 202 <conditional name="ref_source">
202 <param name="source" value="builtin" /> 203 <param name="source" value="builtin" />
203 <param name="ref_fasta_builtin" value="test1" /> 204 <param name="ref_fasta_builtin" value="test1" />
204 </conditional> 205 </conditional>
205 <param name="gvcf" value="true"/> 206 <param name="gvcf" value="true"/>
206 <param name="output_files" value="full_alignment,pileup,phased_bam"/> 207 <param name="output_files" value="full_alignment,pileup,phased_vcf"/>
207 <section name="adv"> 208 <section name="adv">
208 <param name="print_ref_calls" value="true"/> 209 <param name="print_ref_calls" value="true"/>
210 <param name="enable_phasing" value="true"/>
209 </section> 211 </section>
210 <output name="merge_output" decompress="true" file="merge_output_1.vcf.gz" ftype="vcf_bgzip"/> 212 <output name="merge_output" decompress="true" file="merge_output_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
211 <output name="pileup" decompress="true" file="pileup_1.vcf.gz" ftype="vcf_bgzip"/> 213 <output name="pileup" decompress="true" file="pileup_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
212 <output name="full_alignment" decompress="true" file="full_alignment_1.vcf.gz" ftype="vcf_bgzip"/> 214 <output name="full_alignment" decompress="true" file="full_alignment_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
213 <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"/>
214 </test> 216 </test>
217 <!-- test3 -->
215 <test expect_num_outputs="4"> 218 <test expect_num_outputs="4">
216 <conditional name="model_source"> 219 <conditional name="model_source">
217 <param name="source" value="datatable" /> 220 <param name="source" value="datatable" />
218 <param name="model" value="test_model" /> 221 <param name="model" value="test_model" />
219 </conditional> 222 </conditional>
224 </conditional> 227 </conditional>
225 <conditional name="ref_source"> 228 <conditional name="ref_source">
226 <param name="source" value="builtin" /> 229 <param name="source" value="builtin" />
227 <param name="ref_fasta_builtin" value="test1" /> 230 <param name="ref_fasta_builtin" value="test1" />
228 </conditional> 231 </conditional>
229 <param name="output_files" value="full_alignment,pileup,phased_bam"/> 232 <param name="output_files" value="full_alignment,pileup,phased_vcf"/>
230 <section name="adv"> 233 <section name="adv">
231 <param name="snp_min_af" value="0.5"/> 234 <param name="snp_min_af" value="0.5"/>
232 <param name="indel_min_af" value="0.12"/> 235 <param name="indel_min_af" value="0.12"/>
233 <param name="no_phasing_for_fa" value="true" /> 236 <param name="no_phasing_for_fa" value="true" />
234 <param name="print_ref_calls" value="true"/> 237 <param name="print_ref_calls" value="true"/>
235 </section> 238 </section>
236 <output name="merge_output" ftype="vcf_bgzip"> 239 <output name="merge_output" decompress="true" ftype="vcf_bgzip">
237 <assert_contents> 240 <assert_contents>
238 <has_size value="450" delta="50" /> 241 <has_text text="#CHROM" />
239 </assert_contents> 242 </assert_contents>
240 </output> 243 </output>
241 <output name="pileup" ftype="vcf_bgzip"> 244 <output name="pileup" ftype="vcf_bgzip">
242 <assert_contents> 245 <assert_contents>
243 <has_size value="0" /> 246 <has_size value="0" />
246 <output name="full_alignment" ftype="vcf_bgzip"> 249 <output name="full_alignment" ftype="vcf_bgzip">
247 <assert_contents> 250 <assert_contents>
248 <has_size value="0" /> 251 <has_size value="0" />
249 </assert_contents> 252 </assert_contents>
250 </output> 253 </output>
251 <output name="phased_bam" ftype="bam"> 254 <output name="phased_vcf" ftype="vcf_bgzip">
252 <assert_contents> 255 <assert_contents>
253 <has_size value="0" /> 256 <has_size value="0" />
254 </assert_contents> 257 </assert_contents>
255 </output> 258 </output>
256 </test> 259 </test>
260 <!-- test4 -->
257 <!-- Test input CRAM --> 261 <!-- Test input CRAM -->
258 <test expect_num_outputs="1"> 262 <test expect_num_outputs="1">
259 <conditional name="model_source"> 263 <conditional name="model_source">
260 <param name="source" value="builtin" /> 264 <param name="source" value="built-in" />
261 <param name="select_built_in" value="r941_prom_hac_g360+g422" /> 265 <param name="select_built_in" value="r941_prom_hac_g360+g422" />
262 </conditional> 266 </conditional>
263 <param name="bam_input" value="test1.cram" /> 267 <param name="bam_input" value="test1.cram" />
264 <conditional name="ref_source"> 268 <conditional name="ref_source">
265 <param name="source" value="history" /> 269 <param name="source" value="history" />
266 <param name="ref_fasta" value="test1.fasta" /> 270 <param name="ref_fasta" value="test1.fasta" />
267 </conditional> 271 </conditional>
268 <output name="merge_output" file="output_cram_test.vcf.gz" ftype="vcf_bgzip"/> 272 <output name="merge_output" decompress="true" file="output_cram_test.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
269 </test> 273 </test>
270 </tests> 274 </tests>
271 <help><![CDATA[ 275 <help><![CDATA[
272 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:
273 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.