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planemo upload for repository https://github.com/galaxyproject/tools-iuc commit d2d7bf4fbdd781458833134cee92c46ff6a4f603
author iuc
date Tue, 24 Sep 2024 19:30:03 +0000
parents 93c4b04a0769
children 09f5c6f3088a
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0:93c4b04a0769 1:3f6f028f418f
1 <tool id="sniffles" name="sniffles" version="@TOOL_VERSION@+galaxy0"> 1 <tool id="sniffles" name="sniffles" version="@TOOL_VERSION@+galaxy0" profile="23.0">
2 <description>Structural variation caller using third generation sequencing</description> 2 <description>Structural variation caller using third generation sequencing</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.0.12</token> 4 <token name="@TOOL_VERSION@">2.4</token>
5 </macros> 5 </macros>
6 <xrefs>
7 <xref type="bio.tools">sniffles</xref>
8 </xrefs>
6 <requirements> 9 <requirements>
7 <requirement type="package" version="@TOOL_VERSION@">sniffles</requirement> 10 <requirement type="package" version="@TOOL_VERSION@">sniffles</requirement>
8 </requirements> 11 </requirements>
9 <version_command> 12 <version_command>
10 <![CDATA[ sniffles --version ]]> 13 <![CDATA[ sniffles --version ]]>
11 </version_command> 14 </version_command>
12 <command detect_errors="exit_code"> 15 <command detect_errors="exit_code">
13 <![CDATA[ 16 <![CDATA[
14 ln -f -s '${input}' input.bam && 17 ln -f -s '${input}' input.bam &&
15 ln -f -s '${input.metadata.bam_index}' input.bam.bai && 18 ln -f -s '${input.metadata.bam_index}' input.bam.bai &&
16
17 sniffles 19 sniffles
18 -t \${GALAXY_SLOTS:-2} 20 -t \${GALAXY_SLOTS:-2}
19 -m 'input.bam' 21 -i 'input.bam'
20 -v '$output' 22 -v '$output'
23 ## must set allow-overwrite since the new output vcf file exists
24 --allow-overwrite
25 #if $reference_genome.genome_type_select != "None":
26 #if $reference_genome.genome_type_select == "indexed":
27 --reference '${reference_genome.genome.fields.path}'
28 #else:
29 --reference '${reference_genome.genome}'
30 #end if
31 #end if
21 ## general_options 32 ## general_options
22 #if $general_options.min_support: 33 --minsupport '$general_options.minsupport'
23 --min_support $general_options.min_support 34 --max-splits-kb '$general_options.maxsplitskb'
24 #end if 35 --minsvlen '$general_options.minsvlen'
25 --max_num_splits $general_options.max_num_splits 36 --mapq '$general_options.mapq'
26 #if $general_options.max_distance: 37 --min-alignment-length '$general_options.minalignmentlength'
27 --max_distance $general_options.max_distance
28 #end if
29 #if $general_options.min_length:
30 --min_length $general_options.min_length
31 #end if
32 --minmapping_qual $general_options.minmapping_qual
33 --num_reads_report $general_options.num_reads_report
34 #if $general_options.min_seq_size:
35 --min_seq_size $general_options.min_seq_size
36 #end if
37 --min_zmw $general_options.min_zmw
38 $general_options.cs_string
39 ## clustering_options 38 ## clustering_options
40 $clustering_options.cluster 39 --cluster-binsize '$clustering_options.clusterbinsize'
41 #if $clustering_options.cluster_support: 40 --cluster-r '$clustering_options.clusterr'
42 --cluster_support $clustering_options.cluster_support 41 ## advanced_options
43 #end if 42 $advanced_options.mosaic
44 --allelefreq $clustering_options.allelefreq
45 --min_homo_af $clustering_options.min_homo_af
46 --min_het_af $clustering_options.min_het_af
47 ##advanced_options
48 $advanced_options.report_BND
49 $advanced_options.not_report_seq
50 $advanced_options.ignore_sd
51 $advanced_options.ccs_reads
52 ## parameter_estimation_options
53 $parameter_estimation_options.skip_parameter_estimation
54 --del_ratio $parameter_estimation_options.del_ratio
55 --ins_ratio $parameter_estimation_options.ins_ratio
56 --max_diff_per_window $parameter_estimation_options.max_diff_per_window
57 --max_dist_aln_events $parameter_estimation_options.max_dist_aln_events
58 ]]> 43 ]]>
59 </command> 44 </command>
60 <inputs> 45 <inputs>
61 <param type="data" name="input" format="bam" label="Input BAM file"/> 46 <param type="data" name="input" format="bam" label="Input BAM file"/>
47 <conditional name="reference_genome">
48 <param name="genome_type_select" type="select" label="Reference genome source is required for deletion SV sequence reporting"
49 help="Optional: Select None, a built-in or history reference genome fasta">
50 <option value="None" selected="True">No reference fasta - do not report DEL SV sequence</option>
51 <option value="indexed">Use a Galaxy server built-in genome</option>
52 <option value="history">Use a genome fasta file from the current history</option>
53 </param>
54 <when value="None">
55 <param name="genome" type="text" value="None"/>
56 </when>
57 <when value="indexed">
58 <param name="genome" type="select" optional="false" label="Select a built in reference genome or custom genome"
59 help="If not listed, add a custom genome or use a reference genome from the history">
60 <options from_data_table="all_fasta">
61 <validator message="No genomes are available " type="no_options"/>
62 </options>
63 </param>
64 </when>
65 <when value="history">
66 <param name="genome" type="data" format="fasta" optional="false" label="Select the reference genome fasta from the current history"/>
67 </when>
68 </conditional>
62 <section name="general_options" title="Set general options" expanded="False"> 69 <section name="general_options" title="Set general options" expanded="False">
63 <param argument="--min_support" type="integer" value="10" optional="true" min="1" label="Minimum Support" help="Minimum number of reads that support a SV. [10]" /> 70 <param argument="--minsupport" type="text" value="auto" label="Minimum Support" help="Minimum number of reads that support a SV. [auto]. Smaller support values -> more SV reported"/>
64 <param argument="--max_num_splits" type="integer" value="7" optional="true" min="0" label="Maximum Number of Splits" help="Maximum number of splits per read to be still taken into account. [7]" /> 71 <param name="maxsplitskb" type="float" value="0.1" min="0" label="Maximum Number of Splits per KB" help="Additional number of splits per kilobase read sequence allowed before reads are ignored [0.1]" />
65 <param argument="--max_distance" type="integer" value="1000" optional="true" min="10" label="Maximum Distance" help="Maximum distance to group SV together. [1000]" /> 72 <param name="minsvlen" type="integer" value="50" min="2" label="Minimum Length" help="Minimum length of SV to be reported. [50]"/>
66 <param argument="--min_length" type="integer" value="30" optional="true" min="2" label="Minimum Length" help="Minimum length of SV to be reported. [30]"/> 73 <param name="mapq" type="integer" value="20" min="0" label="Minimum Mapping Quality" help="Minimum Mapping Quality to consider. [20]"/>
67 <param argument="--minmapping_qual" type="integer" value="20" optional="true" min="0" label="Minimum Mapping Quality" help="Minimum Mapping Quality. [20]"/> 74 <param name="minalignmentlength" type="integer" value="100" min="0" label="Minimum alignment length" help="Reads with alignments shorter than this length (in bp) will be ignored"/>
68 <param argument="--num_reads_report" type="integer" value="0" optional="true" min="-1" label="Number of reads to report" help="Report up to N reads that support the SV in the vcf file. -1: report all. [0]"/>
69 <param argument="--min_seq_size" type="integer" value="" optional="true" label="Minimum Seq Size" help="Discard read if non of its segment is larger then this. [2000]"/>
70 <param argument="--min_zmw" type="integer" value="0" optional="true" min="0" label="Minimum ZMW" help="Discard SV that are not supported by at least x zmws. This applies only for PacBio recognizable reads. [0]"/>
71 <param argument="--cs_string" type="boolean" truevalue="--cs_string" falsevalue="" optional="true" label="Enable CS String" help="Enables the scan of CS string instead of Cigar and MD. [false]"/>
72 </section> 75 </section>
73 <section name="clustering_options" title="Clustering/phasing and genotyping options" expanded="False"> 76 <section name="clustering_options" title="Clustering/phasing and genotyping options" expanded="False">
74 <param argument="--cluster" type="boolean" truevalue="--cluster" falsevalue="" optional="true" label="Cluster" help="Enables Sniffles to phase SVs that occur on the same reads [false]"/> 77 <param argument="--clusterbinsize" value="100" type="integer" min="0" label="Cluster bin size" help="Initial screening bin size [100]"/>
75 <param argument="--cluster_support" type="integer" value="1" optional="true" min="1" label="Cluster Support" help="Minimum number of reads supporting clustering of SV. [1]"/> 78 <param argument="--clusterr" type="float" value="2.5" min="0.0" label="Cluster Multiplier" help="Multiplier for SV start position standard deviation criterion in cluster merging [2.5]"/>
76 <param argument="--allelefreq" type="float" value="0" optional="true" min="0" label="Allele Frequency Threshold" help="Filters the SV calls based on the allele frequency. [0]" />
77 <param argument="--min_homo_af" type="float" value="0.8" optional="true" min="0" max="1" label="Minimum Homogenous Allele Frequency" help="Minimum homogeneous threshold on allele frequency (0-1). [0.8]"/>
78 <param argument="--min_het_af" type="float" value="0.3" optional="true" min="0" max="1" label="Minimum Heterogeneous Allele Frequency" help="Minimum heterogeneous threshold on allele frequency (0-1). [0.3]"/>
79 </section> 79 </section>
80 <section name="advanced_options" title="Advanced options" expanded="False"> 80 <section name="advanced_options" title="Advanced options" expanded="False">
81 <param argument="--report_BND" type="boolean" value="True" truevalue="--report_BND" falsevalue="" optional="true" label="Report BND" help="Report BND instead of Tra in vcf output. [true]" /> 81 <param name="mosaic" type="boolean" value="False" truevalue="--mosaic" falsevalue="" label="Mosaic mode" help="Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)" />
82 <param argument="--not_report_seq" type="boolean" value="False" truevalue="--not_report_seq" falsevalue="" optional="true" label="Don't report seq" help="Don't report sequences for indels in vcf output. (Beta version!) [false]"/>
83 <param argument="--ignore_sd" type="boolean" value="False" truevalue="--ignore_sd" falsevalue="" optional="true" label="Igonore sd" help="Ignores the sd based filtering. [false]"/>
84 <param argument="--ccs_reads" type="boolean" value="False" truevalue="--ccs_reads" falsevalue="" optional="true" label="CCS Reads" help="Preset CCS Pacbio setting. (Beta) [false]" />
85 </section>
86 <section name="parameter_estimation_options" title="Parameter Estimation Options" expanded="False">
87 <param argument="--skip_parameter_estimation" type="boolean" value="False" truevalue="--skip_parameter_estimation" falsevalue="" optional="true" label="Skip Parameter Estimation" help="Enables the scan if only very few reads are present. [false]"/>
88 <param argument="--del_ratio" type="float" value="0.0458369" optional="true" min="0" max="1" label="Estimated Deletion Ratio" help="Estimated ratio of deletions per read (0-1). [0.0458369]" />
89 <param argument="--ins_ratio" type="float" value="0.049379" optional="true" min="0" max="1" label="Estimated Insertion Ratio" help="Estimated ratio of insertions per read (0-1). [0.049379]" />
90 <param argument="--max_diff_per_window" type="integer" value="50" optional="true" min="0" label="Maximum Differences Per Window" help="Maximum differences per 100bp. [50]"/>
91 <param argument="--max_dist_aln_events" type="integer" value="4" optional="true" min="0" label="Maximum Distance Between Alignment Events" help="Maximum distance between alignment (indel) events. [4]"/>
92 </section> 82 </section>
93 </inputs> 83 </inputs>
94 <outputs> 84 <outputs>
95 <data name="output" format="vcf" label="${tool.name} on ${on_string}"/> 85 <data name="output" format="vcf" label="${tool.name} on ${on_string}"/>
96 </outputs> 86 </outputs>
97 <tests> 87 <tests>
98 <test> <!-- test 1 - standard run --> 88 <test> <!-- test 1 - standard run -->
99 <param name="input" value="reads_region.bam"/> 89 <param name="input" value="reads_region.bam"/>
100 <param name="output_format" value="vcf"/> 90 <output name="output" file="expected_output.vcf" lines_diff="4"/>
101 <output name="output" file="expected_output.vcf" lines_diff="2"/> 91 </test>
102 </test> 92 <test> <!-- test 2 - filter on mapq -->
103 <test> <!-- test 2 - add reads into report --> 93 <param name="input" value="reads_region.bam"/>
104 <param name="input" value="reads_region.bam"/> 94 <param name="mapq" value="0"/>
105 <param name="output_format" value="vcf"/> 95 <output name="output" file="expected_output2.vcf" lines_diff="4"/>
106 <param name="num_reads_report" value="-1"/> 96 </test>
107 <output name="output" file="expected_output2.vcf" lines_diff="2"/> 97 <test> <!-- test 3 min support test -->
108 </test> 98 <param name="input" value="reads_region.bam"/>
109 <test> <!-- test 3 - use cs_string --> 99 <param name="minsupport" value="1"/>
110 <param name="input" value="reads_region.bam"/> 100 <output name="output" file="expected_outcome3.vcf" lines_diff="4"/>
111 <param name="output_format" value="vcf"/>
112 <param name="cs_string" value="true"/>
113 <output name="output" file="expected_outcome3.vcf" lines_diff="2"/>
114 </test> 101 </test>
115 <test> <!-- test 4 - clustering --> 102 <test> <!-- test 4 - clustering -->
116 <param name="input" value="reads_region.bam"/> 103 <param name="input" value="reads_region.bam"/>
117 <param name="output_format" value="vcf"/> 104 <param name="clusterbinsize" value="5"/>
118 <param name="cluster" value="True"/> 105 <output name="output" file="expected_outcome4.vcf" lines_diff="4"/>
119 <output name="output" file="expected_outcome4.vcf" lines_diff="2"/> 106 </test>
120 </test> 107 <test> <!-- test 5 - Advanced - mosaic -->
121 <test> <!-- test 5 - Advanced - Report BND --> 108 <param name="input" value="reads_region.bam"/>
122 <param name="input" value="reads_region.bam"/> 109 <param name="mosaic" value="--mosaic"/>
123 <param name="output_format" value="vcf"/> 110 <output name="output" file="expected_outcome5.vcf" lines_diff="4"/>
124 <param name="report_BND" value="True"/>
125 <output name="output" file="expected_outcome5.vcf" lines_diff="2"/>
126 </test>
127 <test> <!-- test 6 - Parameter Estimation - skip -->
128 <param name="input" value="reads_region.bam"/>
129 <param name="output_format" value="vcf"/>
130 <param name="skip_parameter_estimation" value="True"/>
131 <output name="output" file="expected_outcome6.vcf" lines_diff="2"/>
132 </test> 111 </test>
133 </tests> 112 </tests>
134 <help> 113 <help>
135 <![CDATA[ 114 <![CDATA[
136 ######## 115 ########
137 Sniffles 116 Sniffles
138 ######## 117 ########
139 118
140 What is Sniffles? 119 What is Sniffles?
141 ***************** 120 *****************
142 Sniffles is a SV caller for long reads. It is mainly designed for PacBio reads, but also works on Oxford Nanopore reads. SV are larger events on the genome (e.g. deletions, duplications, insertions, inversions and translocations). Sniffles can detect all of these type and more such as nested SVs (e.g. inversion flanked by deletions or an inverted duplication). Furthermore, Sniffles incorporates multiple auto tuning functions to determine data set depending parameter to reduce the overall risk of falsely infer SVs. 121 Sniffles is a SV caller for long reads. Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.
143 122
144 Quick Start 123 SV are larger events on the genome (e.g. deletions, duplications, insertions, inversions and translocations).
145 *********** 124 Sniffles can detect all of these type and more such as nested SVs (e.g. inversion flanked by deletions or an inverted duplication).
146 125
147 Make sure you have a sorted bam file either from ngmlr or from bwa. For the later make sure you have used -M parameter for mapping to mark which alignments are primary and which are secondary! Note you have to adjust the parameters for low coverage cases. 126 Inputs
127 ******
128
129 Known to work with Minimap2 bam as input
148 130
149 Parameters 131 Parameters
150 ********** 132 **********
151 133
152 General 134 General
153 ------- 135 -------
154 136
137
155 +---------------------------+-----------------------------------------------------------------------+ 138 +---------------------------+-----------------------------------------------------------------------+
156 | Parameter | Description | 139 | Parameter | Description |
157 +===========================+=======================================================================+ 140 +===========================+=======================================================================+
158 | Minimum Support | Minimum number of reads that support a SV to be reported. Default: 10 | 141 | Minimum Support | Minimum number of reads supporting a SV to be reported. Default:auto |
159 +---------------------------+-----------------------------------------------------------------------+ 142 +---------------------------+-----------------------------------------------------------------------+
160 | Maximum Number of Splits | Maximum number of split segments a read is aligned at before it is | 143 | Maximum Number of Splits | Maximum number of split segments per kb a read is aligned at before |
161 | | ignored. Default: 7 | 144 | | it is ignored. Default: 7 |
162 +---------------------------+-----------------------------------------------------------------------+ 145 +---------------------------+-----------------------------------------------------------------------+
163 | Maximum Distance | Maximum distance to group SV together. Sniffles estimates this | 146 | Minimum SV Length | Minimum length of SV to be reported. Default: 50bp |
164 | | parameter during runtime to group together SVs reported by different |
165 | | reads. Default: 1kb |
166 +---------------------------+-----------------------------------------------------------------------+
167 | Minimum Length | Minimum length of SV to be reported. Default: 30bp |
168 +---------------------------+-----------------------------------------------------------------------+ 147 +---------------------------+-----------------------------------------------------------------------+
169 | Minimum Mapping Quality | Minimum mapping quality of alignment to be taken into account. | 148 | Minimum Mapping Quality | Minimum mapping quality of alignment to be taken into account. |
170 | | Default: 20 | 149 | | Default: 20 |
171 +---------------------------+-----------------------------------------------------------------------+ 150 +---------------------------+-----------------------------------------------------------------------+
172 | Number of Reads to Report | Number of read names to be reported that support the SV in the vcf | 151 | Minimum alignment length | Reads with less length aligned will be ignored. Default 100 |
173 | | file. Default: 0 | 152 +---------------------------+-----------------------------------------------------------------------+
174 +---------------------------+-----------------------------------------------------------------------+ 153
175 | Minimum Seq Size | Discard read if none of its segment is larger then this. Default: 2kb |
176 +---------------------------+-----------------------------------------------------------------------+
177 | Minimum ZMW | Discard SV that are not supported by at least x zmws. This applies |
178 | | only for PacBio recognizable reads. Default: 0 |
179 +---------------------------+-----------------------------------------------------------------------+
180 | Enable CS String | Enables the scan of CS string instead of Cigar and MD. Default: False|
181 +---------------------------+-----------------------------------------------------------------------+
182
183 |
184 154
185 Clustering Options 155 Clustering Options
186 ------------------ 156 ------------------
157
187 158
188 +----------------------------------------+-----------------------------------------------------------------------+ 159 +----------------------------------------+-----------------------------------------------------------------------+
189 | Parameter | Description | 160 | Parameter | Description |
190 +========================================+=======================================================================+ 161 +========================================+=======================================================================+
191 | Cluster | Performs read based phasing to mark SVs that occur together. | 162 | Cluster bin size | Initial cluster bin size. Default 100 |
192 +----------------------------------------+-----------------------------------------------------------------------+ 163 +----------------------------------------+-----------------------------------------------------------------------+
193 | Cluster Support | Minimum number of reads supporting clustering of SV. Default: 1 | 164 | Cluster Multiplier | Multiplier for SV start position standard deviation criterion in |
165 | | cluster merging [2.5] |
194 +----------------------------------------+-----------------------------------------------------------------------+ 166 +----------------------------------------+-----------------------------------------------------------------------+
195 | Allele Frequency Threshold | Filters the SV calls based on the allele frequency. Default: 0.0 | 167
196 +----------------------------------------+-----------------------------------------------------------------------+
197 | Minimum Homogenous Allele Frequency | Minimum homogeneous threshold on allele frequency. Default: 0.8 |
198 +----------------------------------------+-----------------------------------------------------------------------+
199 | Minimum Heterogeneous Allele Frequency | Minimum heterogeneous threshold on allele frequency. Default: 0.3 |
200 +----------------------------------------+-----------------------------------------------------------------------+
201
202 |
203 168
204 Advanced Options 169 Advanced Options
205 ---------------- 170 ----------------
206 171
207 +----------------------------------------+------------------------------------------------------------------------+ 172
208 | Parameter | Description | 173 +----------------------------------------+------------------------------------------------------------------------------+
209 +========================================+========================================================================+ 174 | Parameter | Description |
210 | Report BND | Reports the inversions and translocations as BND events. Default: False| 175 +========================================+==============================================================================+
211 +----------------------------------------+------------------------------------------------------------------------+ 176 | Mosaic | Set Sniffles run mode to detect rare, somatic and mosaic SVs (default: False)|
212 | Don't Report Seq | Don't report sequences for indels in vcf output. (Beta version!) | 177 +----------------------------------------+------------------------------------------------------------------------------+
213 | | Default: False | 178
214 +----------------------------------------+------------------------------------------------------------------------+
215 | Ignore sd | Ignores the sd based filtering. Default: False |
216 +----------------------------------------+------------------------------------------------------------------------+
217 | CCS Reads | Preset CCS Pacbio setting. (Beta) Default: False |
218 +----------------------------------------+------------------------------------------------------------------------+
219
220 |
221
222 Parameter Estimation Options
223 ----------------------------
224
225 +----------------------------------------+------------------------------------------------------------------------+
226 | Parameter | Description |
227 +========================================+========================================================================+
228 | Skip Parameter Estimation | Enables the scan if only very few reads are present. Default: False |
229 +----------------------------------------+------------------------------------------------------------------------+
230 | Estimated Deletion Ratio | Estimated ratio of deletions per read. Default: 0.0458369 |
231 +----------------------------------------+------------------------------------------------------------------------+
232 | Estimated Insertion Ratio | Estimated ratio of insertions per read. Default: 0.049379 |
233 +----------------------------------------+------------------------------------------------------------------------+
234 | Maximum Differences Per Window | Maximum differences per 100bp. Default: 50 |
235 +----------------------------------------+------------------------------------------------------------------------+
236 | Maximum Distance Between Alignment | Maximum distance between alignment (indel) events. Default: 4 |
237 | Events | |
238 +----------------------------------------+------------------------------------------------------------------------+
239
240 |
241 179
242 Output 180 Output
243 ****** 181 ******
244 182
245 VCF Info field description 183 VCF Info field description
246 | 184
247 Sniffles report multiple information in the Info field. The entries are delimited by: 185 Sniffles report multiple information in the Info field. The entries are delimited by:
248 | 186
249 +-------------------+------------------------------------------------------------------------------------------------------+ 187 +-------------------+------------------------------------------------------------------------------------------------------+
250 | IMPRECISE/PRECISE | Indicates the confidence of the exact breakpoint positions (bp). | 188 | IMPRECISE/PRECISE | Indicates the confidence of the exact breakpoint positions (bp). |
251 +-------------------+------------------------------------------------------------------------------------------------------+ 189 +-------------------+------------------------------------------------------------------------------------------------------+
252 | CHR2= | The chromosome of the second breakpoint of the SV reported. | 190 | CHR2= | The chromosome of the second breakpoint of the SV reported. |
253 +-------------------+------------------------------------------------------------------------------------------------------+ 191 +-------------------+------------------------------------------------------------------------------------------------------+
273 +-------------------+------------------------------------------------------------------------------------------------------+ 211 +-------------------+------------------------------------------------------------------------------------------------------+
274 | RE= | Number of reads supporting the variance. | 212 | RE= | Number of reads supporting the variance. |
275 +-------------------+------------------------------------------------------------------------------------------------------+ 213 +-------------------+------------------------------------------------------------------------------------------------------+
276 | AF= | Allele frequency (only if run with –genotype) | 214 | AF= | Allele frequency (only if run with –genotype) |
277 +-------------------+------------------------------------------------------------------------------------------------------+ 215 +-------------------+------------------------------------------------------------------------------------------------------+
278 | 216
279 Source: https://github.com/fritzsedlazeck/Sniffles/wiki 217 Source: https://github.com/fritzsedlazeck/Sniffles
280 ]]> 218 ]]>
281 </help> 219 </help>
282 <citations> 220 <citations>
283 <citation type="doi">10.1038/s41592-018-0001-7</citation> 221 <citation type="doi">10.1038/s41587-023-02024-y</citation>
284 </citations> 222 </citations>
285 </tool> 223 </tool>