clair3: clair3.xml annotate

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

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

rev	line source
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	1 <tool id="clair3" name="Clair3" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.2">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	2 <description>germline small variant caller for long-reads</description>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	3 <macros>
3 2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	4 <token name="@TOOL_VERSION@">1.0.10</token>
2 44914678d18f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 79c3c1123428c177bf4a8c38260232810457845d iuc parents: 1 diff changeset	5 <token name="@VERSION_SUFFIX@">1</token>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	6 </macros>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	7 <xrefs>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	8 <xref type='bio.tools'>clair3</xref>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	9 </xrefs>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	10 <requirements>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	11 <requirement type="package" version="@TOOL_VERSION@">clair3</requirement>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	12 </requirements>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	13 <version_command><![CDATA[run_clair3.sh --version \| cut -f2 -d ' ']]></version_command>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	14 <command detect_errors="exit_code"><![CDATA[
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	15 #if $ref_source.source == "history"
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	16 ln -s '${ref_source.ref_fasta}' reference.fasta &&
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	17 #elif $ref_source.source == "builtin"
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	18 ln -s '${ref_source.ref_fasta_builtin.fields.path}' reference.fasta &&
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	19 #end if
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	20 samtools faidx reference.fasta &&
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	21
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	22 #if $model_source.source == "datatable"
3 2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	23 #set model_path = $model_source.model.fields.path
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	24 #if $model_source.model.fields.source == "rerio" and $ont_license_agree != "true"
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	25 echo "You must agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement to use Rerio models." >&2 &&
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	26 exit 2 ;
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	27 #end if
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	28 #end if
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	29 #set $extension = $bam_input.ext
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	30 ln -s '${$bam_input}' input_reads.$extension &&
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	31 #if $extension == 'bam'
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	32 ln -s '${$bam_input.metadata.bam_index}' input_reads.bai &&
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	33 #else
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	34 ln -s '${$bam_input.metadata.cram_index}' input_reads.crai &&
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	35 #end if
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	36
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	37 #if $bed_or_vcf.bed_or_vcf_selector == 'bed'
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	38 ln -s '$bed_or_vcf.bed_fn' input.bed &&
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	39 #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf'
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	40 ln -s '$bed_or_vcf.vcf_fn' input.vcf &&
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	41 #end if
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	42
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	43 run_clair3.sh
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	44 --bam_fn=input_reads.$extension
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	45 --ref_fn=reference.fasta
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	46 #if $model_source.source == "datatable"
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	47 --platform='${model_source.model.fields.platform}'
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	48 --model_path=${model_source.model.fields.path}
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	49 #else
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	50 #if $model_source.select_built_in == "hifi" or $model_source.select_built_in == "ilmn":
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	51 --platform='${$model_source.select_built_in}'
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	52 #else
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	53 --platform='ont'
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	54 #end if
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	55 --model_path=\$(dirname \$(which run_clair3.sh))/models/$model_source.select_built_in
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	56 #end if
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	57 --output='.'
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	58 --threads=\${GALAXY_SLOTS:-2}
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	59 #if $bed_or_vcf.bed_or_vcf_selector == 'bed'
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	60 --bed_fn=input.bed
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	61 #elif $bed_or_vcf.bed_or_vcf_selector == 'vcf'
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	62 --vcf_fn=input.vcf
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	63 #else
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	64 $bed_or_vcf.include_all_ctgs
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	65 #end if
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	66 $gvcf
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	67 #if $adv.qual
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	68 --qual=$adv.qual
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	69 #end if
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	70 #if $adv.snp_min_af
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	71 --snp_min_af=$adv.snp_min_af
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	72 #end if
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	73 #if $adv.indel_min_af
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	74 --indel_min_af=$adv.indel_min_af
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	75 #end if
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	76 $adv.enable_phasing
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	77 $adv.no_phasing_for_fa
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	78 $adv.print_ref_calls
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	79 $adv.ploidity_model
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	80 #if $adv.chunk_size
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	81 --chunk_size=$adv.chunk_size
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	82 #end if
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	83 ]]></command>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	84 <inputs>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	85 <param type="data" name="bam_input" argument="--bam_fn" format="bam,cram" label="BAM/CRAM file input" />
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	86 <conditional name="ref_source">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	87 <param type="select" label="Reference genome source" name="source">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	88 <option value="history" selected="true">History</option>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	89 <option value="builtin">Built-in</option>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	90 </param>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	91 <when value="history">
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	92 <param type="data" format="fasta" name="ref_fasta" argument="--ref_fn" label="Reference genome" />
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	93 </when>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	94 <when value="builtin">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	95 <param type="select" name="ref_fasta_builtin" label="Reference genome">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	96 <options from_data_table="all_fasta" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	97 </param>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	98 </when>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	99 </conditional>
3 2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	100 <param name="ont_license_agree"
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	101 label="I agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement"
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	102 type="boolean" checked="false"
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	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."
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	104 />
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	105 <conditional name="model_source">
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	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.">
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	107 <option value="built-in">Built-in</option>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	108 <option value="datatable">Cached</option>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	109 </param>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	110 <when value="built-in">
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	111 <param type="select" name="select_built_in" label="Built-in model">
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	112 <option value="r941_prom_sup_g5014">r941_prom_sup_g5014</option>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	113 <option value="r941_prom_hac_g360+g422">r941_prom_hac_g360+g422</option>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	114 <option value="hifi">hifi</option>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	115 <option value="ilmn">ilmn</option>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	116 </param>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	117 </when>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	118 <when value="datatable">
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	119 <param name="model" argument="--model_path" type="select" label="Cached model from server" >
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	120 <options from_data_table="clair3_models">
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	121 <validator type="no_options" message="no cached models available" />
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	122 </options>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	123 </param>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	124 </when>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	125 </conditional>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	126 <conditional name="bed_or_vcf">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	127 <param type="select" name="bed_or_vcf_selector" label="Restrict variant calling to:">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	128 <option value="unrestricted" selected="true">Whole reference (unrestricted)</option>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	129 <option value="bed" selected="true">Regions defined in BED dataset</option>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	130 <option value="vcf">Sites defined in VCF dataset</option>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	131 </param>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	132 <when value="bed">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	133 <param type="data" argument="--bed_fn" format="bed" label="Call variants only in the provided bed regions."/>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	134 </when>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	135 <when value="vcf">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	136 <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."/>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	137 </when>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	138 <when value="unrestricted">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	139 <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}" />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	140 </when>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	141 </conditional>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	142 <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" />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	143 <param name="output_files" type="select" display="checkboxes" multiple="true" label="Optional additional output files">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	144 <option value="full_alignment">Full alignment file</option>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	145 <option value="pileup">Pileup file</option>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	146 <option value="phased_vcf">Phased VCF file</option>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	147 </param>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	148 <section name="adv" title="Advanced parameters" expanded="false">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	149 <param type="integer" argument="--qual" value="0" min="0" label="Qual" help="If set, variants with >qual will be marked PASS, or LowQual otherwise." />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	150 <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." />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	151 <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." />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	152 <param type="boolean" argument="--enable_phasing" truevalue="--enable_phasing" falsevalue="" label="Enable phasing" help="Output phased variants using whatshap. Default: disable" />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	153 <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" />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	154 <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." />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	155 <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.">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	156 <option value="" selected="true">Diploid</option>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	157 <option value="--haploid_sensitive">Haploid sensitive (--haploid_sensitive)</option>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	158 <option value="--haploid_precise">haploid precise (--haploid_precise)</option>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	159 </param>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	160 <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" />
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	161 </section>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	162 </inputs>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	163 <outputs>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	164 <data name="merge_output" format="vcf_bgzip" from_work_dir="./merge_output.vcf.gz" label="${tool.name} on ${on_string}: merged output"/>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	165 <data name="pileup" format="vcf_bgzip" from_work_dir="./pileup.vcf.gz" label="${tool.name} on ${on_string}: pileup">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	166 <filter>output_files and 'pileup' in output_files</filter>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	167 </data>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	168 <data name="full_alignment" format="vcf_bgzip" from_work_dir="./full_alignment.vcf.gz" label="${tool.name} on ${on_string}: full alignment">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	169 <filter>output_files and 'full_alignment' in output_files</filter>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	170 </data>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	171 <data name="phased_vcf" format="vcf_bgzip" from_work_dir="./phased_merge_output.vcf.gz" label="${tool.name} on ${on_string}: phased VCF">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	172 <filter>output_files and 'phased_vcf' in output_files</filter>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	173 </data>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	174 </outputs>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	175 <tests>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	176 <!-- test1 -->
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	177 <test expect_num_outputs="1">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	178 <conditional name="model_source">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	179 <param name="source" value="built-in"/>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	180 <param name="select_built_in" value="r941_prom_hac_g360+g422"/>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	181 </conditional>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	182 <param name="bam_input" value="test1.bam" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	183 <conditional name="ref_source">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	184 <param name="source" value="history" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	185 <param name="ref_fasta" value="test1.fasta" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	186 </conditional>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	187 <conditional name="bed_or_vcf">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	188 <param name="bed_or_vcf_selector" value="vcf"/>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	189 <param name="vcf_fn" value="test1.vcf.gz" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	190 </conditional>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	191 <section name="adv">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	192 <param name="no_phasing_for_fa" value="true"/>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	193 <param name="print_ref_calls" value="true"/>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	194 <param name="ploidity_model" value=""/>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	195 </section>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	196 <assert_stdout>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	197 <has_text text="[WARNING] No contig intersection found, output header only in" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	198 </assert_stdout>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	199 </test>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	200 <!-- test2 -->
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	201 <test expect_num_outputs="4">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	202 <conditional name="model_source">
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	203 <param name="source" value="built-in" />
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	204 <param name="select_built_in" value="r941_prom_hac_g360+g422" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	205 </conditional>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	206 <param name="bam_input" value="test1.bam" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	207 <conditional name="bed_or_vcf">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	208 <param name="bed_or_vcf_selector" value="unrestricted"/>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	209 <param name="include_all_ctgs" value="true" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	210 </conditional>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	211 <conditional name="ref_source">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	212 <param name="source" value="builtin" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	213 <param name="ref_fasta_builtin" value="test1" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	214 </conditional>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	215 <param name="gvcf" value="true"/>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	216 <param name="output_files" value="full_alignment,pileup,phased_vcf"/>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	217 <section name="adv">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	218 <param name="print_ref_calls" value="true"/>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	219 <param name="enable_phasing" value="true"/>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	220 </section>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	221 <output name="merge_output" decompress="true" file="merge_output_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	222 <output name="pileup" decompress="true" file="pileup_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	223 <output name="full_alignment" decompress="true" file="full_alignment_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	224 <output name="phased_vcf" decompress="true" file="phased_vcf_1.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	225 </test>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	226 <!-- test3 -->
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	227 <test expect_num_outputs="4">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	228 <conditional name="model_source">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	229 <param name="source" value="datatable" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	230 <param name="model" value="test_model" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	231 </conditional>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	232 <param name="bam_input" value="test1.bam" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	233 <conditional name="bed_or_vcf">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	234 <param name="bed_or_vcf_selector" value="bed"/>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	235 <param name="bed_fn" value="test1.bed" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	236 </conditional>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	237 <conditional name="ref_source">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	238 <param name="source" value="builtin" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	239 <param name="ref_fasta_builtin" value="test1" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	240 </conditional>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	241 <param name="output_files" value="full_alignment,pileup,phased_vcf"/>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	242 <section name="adv">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	243 <param name="snp_min_af" value="0.5"/>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	244 <param name="indel_min_af" value="0.12"/>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	245 <param name="no_phasing_for_fa" value="true" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	246 <param name="print_ref_calls" value="true"/>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	247 </section>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	248 <output name="merge_output" decompress="true" ftype="vcf_bgzip">
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	249 <assert_contents>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	250 <has_text text="#CHROM" />
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	251 </assert_contents>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	252 </output>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	253 <output name="pileup" ftype="vcf_bgzip">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	254 <assert_contents>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	255 <has_size value="0" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	256 </assert_contents>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	257 </output>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	258 <output name="full_alignment" ftype="vcf_bgzip">
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	259 <assert_contents>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	260 <has_size value="0" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	261 </assert_contents>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	262 </output>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	263 <output name="phased_vcf" ftype="vcf_bgzip">
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	264 <assert_contents>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	265 <has_size value="0" />
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	266 </assert_contents>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	267 </output>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	268 </test>
1 bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	269 <!-- test4 -->
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	270 <!-- Test input CRAM -->
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	271 <test expect_num_outputs="1">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	272 <conditional name="model_source">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	273 <param name="source" value="built-in" />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	274 <param name="select_built_in" value="r941_prom_hac_g360+g422" />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	275 </conditional>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	276 <param name="bam_input" value="test1.cram" />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	277 <conditional name="ref_source">
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	278 <param name="source" value="history" />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	279 <param name="ref_fasta" value="test1.fasta" />
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	280 </conditional>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	281 <output name="merge_output" decompress="true" file="output_cram_test.vcf.gz" ftype="vcf_bgzip" lines_diff="4"/>
bd1bbbf7d9b2 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit fa0f3ca0b9b305a017bb37e43fe9b9a897a1149c iuc parents: 0 diff changeset	282 </test>
3 2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	283 <!-- test5 -->
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	284 <!-- Test the working of the ont_license_agree checkbox -->
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	285 <test expect_failure="true" expect_exit_code="2">
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	286 <conditional name="model_source">
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	287 <param name="source" value="datatable" />
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	288 <param name="model" value="r1041_e82_400bps_sup_v500" />
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	289 </conditional>
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	290 <param name="ont_license_agree" value="false" />
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	291 <!-- the rest of the parameters are included for completeness, as this test
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	292 should fail to run because of the license terms conflict -->
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	293 <param name="bam_input" value="test1.bam" />
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	294 <conditional name="ref_source">
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	295 <param name="source" value="history" />
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	296 <param name="ref_fasta" value="test1.fasta" />
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	297 </conditional>
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	298 <conditional name="bed_or_vcf">
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	299 <param name="bed_or_vcf_selector" value="vcf"/>
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	300 <param name="vcf_fn" value="test1.vcf.gz" />
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	301 </conditional>
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	302 <section name="adv">
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	303 <param name="no_phasing_for_fa" value="true"/>
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	304 <param name="print_ref_calls" value="true"/>
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	305 <param name="ploidity_model" value=""/>
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	306 </section>
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	307 <assert_stderr>
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	308 <has_line line="You must agree to the terms of the Oxford Nanopore Technologies, Ltd. Public License agreement to use Rerio models." />
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	309 </assert_stderr>
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	310 </test>
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	311 </tests>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	312 <help><![CDATA[
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	313 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories:
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	314 pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall.
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	315 Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration.
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	316
3 2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	317 The tool can use models from the Oxford Nanopore Technologies Rerio_ repository, which are covered by a license that restricts their use to
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	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,
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	319 which can be found in the Rerio repository in the file LICENSE.txt.
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	320
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	321 https://github.com/HKU-BAL/Clair3
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	322
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	323 LICENSE:
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	324
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	325 Copyright 2021 The University of Hong Kong, Department of Computer Science
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	326
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	327 Redistribution and use in source and binary forms, with or without modification,
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	328 are permitted provided that the following conditions are met:
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	329
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	330 1. Redistributions of source code must retain the above copyright notice, this
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	331 list of conditions and the following disclaimer.
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	332
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	333 2. Redistributions in binary form must reproduce the above copyright notice,
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	334 this list of conditions and the following disclaimer in the documentation
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	335 and/or other materials provided with the distribution.
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	336
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	337 3. Neither the name of the copyright holder nor the names of its contributors
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	338 may be used to endorse or promote products derived from this software without
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	339 specific prior written permission.
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	340
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	341 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	342 ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	343 WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	344 DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	345 ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	346 (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	347 LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	348 ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	349 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	350 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
3 2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	351
2c0989f0990c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit ccc78578217953c215252489b28527182d7c9510 iuc parents: 2 diff changeset	352 .. _Rerio: https://github.com/nanoporetech/rerio
0 a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	353 ]]></help>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	354 <citations>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	355 <citation type="doi">10.1101/2021.12.29.474431</citation>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	356 </citations>
a412acb452ea planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/clair3 commit 9968295e33bad5323ac9cbff8f64c2db35189a5f iuc parents: diff changeset	357 </tool>

Mercurial > repos > iuc > clair3

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