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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 0807bc20cc19d11346d9f0d6c35ab030e14f8493
author iuc
date Mon, 15 Sep 2025 08:25:40 +0000
parents 3aca08f3fd7f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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9d8fd0806572 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 1221a5ddb00b62d789a6df44fae6a876f5cade37
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1 <tool id="cutesv" name="cuteSV" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
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2 <description>detects long-read-based SVs</description>
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9d8fd0806572 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 1221a5ddb00b62d789a6df44fae6a876f5cade37
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3 <macros>
9d8fd0806572 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 1221a5ddb00b62d789a6df44fae6a876f5cade37
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4 <import>macros.xml</import>
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5 </macros>
1
f4ff82917a1d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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6 <xrefs>
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7 <xref type="bio.tools">cuteSV</xref>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">cutesv</requirement>
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4d75ec9a85bd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 0807bc20cc19d11346d9f0d6c35ab030e14f8493
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11 <requirement type="package" version="1.22.1">samtools</requirement>
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12 </requirements>
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13 <command detect_errors="exit_code"><![CDATA[
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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14 ln -s '$input_sample_file' ./sample.bam &&
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15 ln -s '$input_sample_file.metadata.bam_index' ./sample.bam.bai &&
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17 #if str($reference_source.ref_selector) == 'history':
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18 ln -s '$reference_source.ref' ./genome.fa &&
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19 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for cuteSV' >&2 &&
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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20 #else:
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21 ln -s '$reference_source.ref.fields.path' ./genome.fa &&
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22 ln -s '${reference_source.ref.fields.path}.fai' ./genome.fa.fai &&
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23 #end if
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25 cuteSV ./sample.bam ./genome.fa ./output.vcf ./
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26 --threads \${GALAXY_SLOTS:-4}
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27 --batches '$sel_method.adv_settings.batches'
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28 --sample '$sample'
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29 #if $sel_method.adv_settings.report_readid:
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30 --report_readid
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31 #end if
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32 --max_split_parts '$sel_method.adv_settings.max_split_parts'
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33 --min_mapq '$sel_method.adv_settings.min_mapq'
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34 --min_read_len '$sel_method.adv_settings.min_read_len'
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35 --merge_del_threshold '$sel_method.adv_settings.merge_del_threshold'
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36 --merge_ins_threshold '$sel_method.adv_settings.merge_ins_threshold'
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37 --min_support '$sel_method.adv_settings.min_support'
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38 --min_size '$sel_method.adv_settings.min_size'
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39 --max_size '$sel_method.adv_settings.max_size'
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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40 #if $sel_method.adv_settings.genotyping.genotype:
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41 --genotype
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42 #end if
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43 --gt_round '$sel_method.adv_settings.genotyping.gt_round'
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44 --max_cluster_bias_INS '$sel_method.adv_settings.seq_method.max_cluster_bias_INS'
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45 --diff_ratio_merging_INS '$sel_method.adv_settings.seq_method.diff_ratio_merging_INS'
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46 --max_cluster_bias_DEL '$sel_method.adv_settings.seq_method.max_cluster_bias_DEL'
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47 --diff_ratio_merging_DEL '$sel_method.adv_settings.seq_method.diff_ratio_merging_DEL'
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48 --max_cluster_bias_INV '$sel_method.adv_settings.max_cluster_bias_INV'
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49 --max_cluster_bias_DUP '$sel_method.adv_settings.max_cluster_bias_DUP'
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50 --max_cluster_bias_TRA '$sel_method.adv_settings.max_cluster_bias_TRA'
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51 --diff_ratio_filtering_TRA '$sel_method.adv_settings.diff_ratio_filtering_TRA'
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52 ]]></command>
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53 <inputs>
3
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54 <param name="input_sample_file" type="data" format="bam" label="Sample file" help="Sample file in .BAM format."/>
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55 <expand macro="reference_interface" />
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56 <param name="sample" type="text" value="Sample" label="Sample name/id" help="">
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57 <validator type="length" min="1" message="Please enter a sample name/id"/>
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58 <validator type="regex" message="Please enter a sample name/id">.*[^ ].*</validator>
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59 </param>
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60 <conditional name="sel_method">
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61 <param name="meth_selector" type="select" label="Select the sequencing method of the input file" help="">
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62 <option value="pb_clr" selected="True">PacBio continuous long reads</option>
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63 <option value="pb_ccs">PacBio circular consensus sequencing (HiFi)</option>
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64 <option value="pb_ont">ONT</option>
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65 <option value="other">other method</option>
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66 </param>
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67 <when value="pb_clr">
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68 <section name="adv_settings" title="Advanced settings" expanded="false">
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69 <expand macro="adv_shared_1"/>
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70 <expand macro="adv_pb_clr"/>
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71 <expand macro="adv_shared_2"/>
0
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72 </section>
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73 </when>
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74 <when value="pb_ccs">
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75 <section name="adv_settings" title="Advanced settings" expanded="false">
3
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76 <expand macro="adv_shared_1"/>
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77 <expand macro="adv_pb_ccs"/>
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78 <expand macro="adv_shared_2"/>
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79 </section>
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80 </when>
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81 <when value="pb_ont">
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82 <section name="adv_settings" title="Advanced settings" expanded="false">
3
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83 <expand macro="adv_shared_1"/>
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84 <expand macro="adv_ont"/>
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85 <expand macro="adv_shared_2"/>
0
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86 </section>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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87 </when>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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88 <when value="other">
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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89 <section name="adv_settings" title="Advanced settings" expanded="true">
3
3aca08f3fd7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 963634ce66fcee0fe9d4ecd229cafbb2c4be263c
iuc
parents: 2
diff changeset
90 <expand macro="adv_shared_1"/>
3aca08f3fd7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 963634ce66fcee0fe9d4ecd229cafbb2c4be263c
iuc
parents: 2
diff changeset
91 <expand macro="adv_other"/>
3aca08f3fd7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 963634ce66fcee0fe9d4ecd229cafbb2c4be263c
iuc
parents: 2
diff changeset
92 <expand macro="adv_shared_2"/>
0
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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93 </section>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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94 </when>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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95 </conditional>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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96 </inputs>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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97 <outputs>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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98 <data name="out_sample" format="vcf" label="${tool.name} on ${on_string}: output" from_work_dir="output.vcf" />
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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99 </outputs>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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100 <tests>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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101 <test expect_num_outputs="1">
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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102 <conditional name="reference_source">
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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103 <param name="ref_selector" value="history"/>
3
3aca08f3fd7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 963634ce66fcee0fe9d4ecd229cafbb2c4be263c
iuc
parents: 2
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104 <param name="ref" ftype="fasta" value="genome.fasta"/>
0
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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105 </conditional>
3
3aca08f3fd7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 963634ce66fcee0fe9d4ecd229cafbb2c4be263c
iuc
parents: 2
diff changeset
106 <param name="sel_method|meth_selector" value="pb_ccs"/>
3aca08f3fd7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 963634ce66fcee0fe9d4ecd229cafbb2c4be263c
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parents: 2
diff changeset
107 <param name="input_sample_file" ftype="bam" value="sample.bam"/>
0
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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108 <output name="out_sample">
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iuc
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109 <assert_contents>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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110 <has_text text="##fileformat=VCFv4.2"/>
3
3aca08f3fd7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 963634ce66fcee0fe9d4ecd229cafbb2c4be263c
iuc
parents: 2
diff changeset
111 <has_text text="##contig=&lt;ID=chrM,length=16571&gt;"/>
0
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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112 </assert_contents>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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113 </output>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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114 </test>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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115 <test expect_num_outputs="1">
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
116 <conditional name="reference_source">
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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117 <param name="ref_selector" value="cached"/>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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118 <param name="ref" value="test_buildid"/>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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119 </conditional>
3
3aca08f3fd7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 963634ce66fcee0fe9d4ecd229cafbb2c4be263c
iuc
parents: 2
diff changeset
120 <param name="sel_method|meth_selector" value="pb_ccs"/>
3aca08f3fd7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 963634ce66fcee0fe9d4ecd229cafbb2c4be263c
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parents: 2
diff changeset
121 <param name="input_sample_file" ftype="bam" value="sample.bam"/>
0
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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122 <output name="out_sample">
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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123 <assert_contents>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
parents:
diff changeset
124 <has_text text="##fileformat=VCFv4.2"/>
3
3aca08f3fd7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit 963634ce66fcee0fe9d4ecd229cafbb2c4be263c
iuc
parents: 2
diff changeset
125 <has_text text="##contig=&lt;ID=chrM,length=16571&gt;"/>
0
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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126 </assert_contents>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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127 </output>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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128 </test>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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129 </tests>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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130 <help><![CDATA[
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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131 cuteSV
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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132 =============
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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133
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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134 Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools.
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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135
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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136 For more information see the cuteSV documentation_.
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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137
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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138 .. _documentation: https://github.com/tjiangHIT/cuteSV
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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139
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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140 ]]></help>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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141 <citations>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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142 <citation type="doi">10.1186/s13059-020-02107-y</citation>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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143 </citations>
ce199016a201 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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144 </tool>