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comparison clair3.xml @ 3:2c0989f0990c draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510
author iuc
date Wed, 19 Feb 2025 16:18:53 +0000
parents 44914678d18f
children
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2:44914678d18f 3:2c0989f0990c
1 <tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2"> 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@">1.0.8</token> 4 <token name="@TOOL_VERSION@">1.0.10</token>
5 <token name="@VERSION_SUFFIX@">1</token> 5 <token name="@VERSION_SUFFIX@">1</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>
18 ln -s '${ref_source.ref_fasta_builtin.fields.path}' reference.fasta && 18 ln -s '${ref_source.ref_fasta_builtin.fields.path}' reference.fasta &&
19 #end if 19 #end if
20 samtools faidx reference.fasta && 20 samtools faidx reference.fasta &&
21 21
22 #if $model_source.source == "datatable" 22 #if $model_source.source == "datatable"
23 #set model_path = $model_source.model.fields.path 23 #set model_path = $model_source.model.fields.path
24 #if $model_source.model.fields.source == "rerio" and $ont_license_agree != "true"
25 echo "You must agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement to use Rerio models." >&2 &&
26 exit 2 ;
27 #end if
24 #end if 28 #end if
25 #set $extension = $bam_input.ext 29 #set $extension = $bam_input.ext
26 ln -s '${$bam_input}' input_reads.$extension && 30 ln -s '${$bam_input}' input_reads.$extension &&
27 #if $extension == 'bam' 31 #if $extension == 'bam'
28 ln -s '${$bam_input.metadata.bam_index}' input_reads.bai && 32 ln -s '${$bam_input.metadata.bam_index}' input_reads.bai &&
91 <param type="select" name="ref_fasta_builtin" label="Reference genome"> 95 <param type="select" name="ref_fasta_builtin" label="Reference genome">
92 <options from_data_table="all_fasta" /> 96 <options from_data_table="all_fasta" />
93 </param> 97 </param>
94 </when> 98 </when>
95 </conditional> 99 </conditional>
100 <param name="ont_license_agree"
101 label="I agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement"
102 type="boolean" checked="false"
103 help="To use Rerio models (e.g. for ONT R10 chemistry) you must agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement, which can be found in the nanoporetech/rerio Github repository."
104 />
96 <conditional name="model_source"> 105 <conditional name="model_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."> 106 <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.">
98 <option value="built-in">Built-in</option> 107 <option value="built-in">Built-in</option>
99 <option value="datatable">Cached</option> 108 <option value="datatable">Cached</option>
100 </param> 109 </param>
269 <param name="source" value="history" /> 278 <param name="source" value="history" />
270 <param name="ref_fasta" value="test1.fasta" /> 279 <param name="ref_fasta" value="test1.fasta" />
271 </conditional> 280 </conditional>
272 <output name="merge_output" decompress="true" file="output_cram_test.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/> 281 <output name="merge_output" decompress="true" file="output_cram_test.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
273 </test> 282 </test>
283 <!-- test5 -->
284 <!-- Test the working of the ont_license_agree checkbox -->
285 <test expect_failure="true" expect_exit_code="2">
286 <conditional name="model_source">
287 <param name="source" value="datatable" />
288 <param name="model" value="r1041_e82_400bps_sup_v500" />
289 </conditional>
290 <param name="ont_license_agree" value="false" />
291 <!-- the rest of the parameters are included for completeness, as this test
292 should fail to run because of the license terms conflict -->
293 <param name="bam_input" value="test1.bam" />
294 <conditional name="ref_source">
295 <param name="source" value="history" />
296 <param name="ref_fasta" value="test1.fasta" />
297 </conditional>
298 <conditional name="bed_or_vcf">
299 <param name="bed_or_vcf_selector" value="vcf"/>
300 <param name="vcf_fn" value="test1.vcf.gz" />
301 </conditional>
302 <section name="adv">
303 <param name="no_phasing_for_fa" value="true"/>
304 <param name="print_ref_calls" value="true"/>
305 <param name="ploidity_model" value=""/>
306 </section>
307 <assert_stderr>
308 <has_line line="You must agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement to use Rerio models." />
309 </assert_stderr>
310 </test>
274 </tests> 311 </tests>
275 <help><![CDATA[ 312 <help><![CDATA[
276 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: 313 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories:
277 pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. 314 pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall.
278 Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. 315 Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.
279 316
317 The tool can use models from the Oxford Nanopore Technologies Rerio_ repository, which are covered by a license that restricts their use to
318 non-commercial use. If you select one of these models, you must agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License,
319 which can be found in the Rerio repository in the file LICENSE.txt.
320
280 https://github.com/HKU-BAL/Clair3 321 https://github.com/HKU-BAL/Clair3
281 322
282 LICENSE: 323 LICENSE:
283 324
284 Copyright 2021 The University of Hong Kong, Department of Computer Science 325 Copyright 2021 The University of Hong Kong, Department of Computer Science
305 (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; 346 (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
306 LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON 347 LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
307 ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT 348 ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
308 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS 349 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
309 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. 350 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
351
352 .. _Rerio: https://github.com/nanoporetech/rerio
310 ]]></help> 353 ]]></help>
311 <citations> 354 <citations>
312 <citation type="doi">10.1101/2021.12.29.474431</citation> 355 <citation type="doi">10.1101/2021.12.29.474431</citation>
313 </citations> 356 </citations>
314 </tool> 357 </tool>