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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
author iuc
date Thu, 24 Sep 2020 15:11:57 +0000
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c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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1 <tool id="cutesv" name="cuteSV" version="@WRAPPER_VERSION@">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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2 <description>detects long-read-based SVs</description>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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3 <macros>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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4 <import>macros.xml</import>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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5 </macros>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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6 <requirements>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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7 <requirement type="package" version="@TOOL_VERSION@">cutesv</requirement>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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8 <requirement type="package" version="1.10">samtools</requirement>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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9 </requirements>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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10 <command detect_errors="exit_code"><![CDATA[
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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11 ln -s '$input_sample_file' ./sample.bam &&
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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12 ln -s '$input_sample_file.metadata.bam_index' ./sample.bam.bai &&
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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13
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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14 #if str($reference_source.ref_selector) == 'history':
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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15 ln -s '$reference_source.ref' ./genome.fa &&
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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16 samtools faidx ./genome.fa 2>&1 || echo 'Error running samtools faidx for indexing fasta reference for cuteSV' >&2 &&
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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17 #else:
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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18 ln -s '$reference_source.ref.fields.path' ./genome.fa &&
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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19 ln -s '${reference_source.ref.fields.path}.fai' ./genome.fa.fai &&
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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20 #end if
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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21
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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22 cuteSV ./sample.bam ./genome.fa ./output.vcf ./
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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23 --threads \${GALAXY_SLOTS:-4}
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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24 --batches '$sel_method.adv_settings.batches'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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25 --sample '$sample'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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26 #if $sel_method.adv_settings.report_readid:
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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27 --report_readid
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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28 #end if
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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29 --max_split_parts '$sel_method.adv_settings.max_split_parts'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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30 --min_mapq '$sel_method.adv_settings.min_mapq'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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31 --min_read_len '$sel_method.adv_settings.min_read_len'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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32 --merge_del_threshold '$sel_method.adv_settings.merge_del_threshold'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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33 --merge_ins_threshold '$sel_method.adv_settings.merge_ins_threshold'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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34 --min_support '$sel_method.adv_settings.min_support'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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35 --min_size '$sel_method.adv_settings.min_size'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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36 --max_size '$sel_method.adv_settings.max_size'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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37 #if $sel_method.adv_settings.genotyping.genotype:
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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38 --genotype
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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39 #end if
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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40 --gt_round '$sel_method.adv_settings.genotyping.gt_round'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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41 --max_cluster_bias_INS '$sel_method.adv_settings.seq_method.max_cluster_bias_INS'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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42 --diff_ratio_merging_INS '$sel_method.adv_settings.seq_method.diff_ratio_merging_INS'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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43 --max_cluster_bias_DEL '$sel_method.adv_settings.seq_method.max_cluster_bias_DEL'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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44 --diff_ratio_merging_DEL '$sel_method.adv_settings.seq_method.diff_ratio_merging_DEL'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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45 --max_cluster_bias_INV '$sel_method.adv_settings.max_cluster_bias_INV'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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46 --max_cluster_bias_DUP '$sel_method.adv_settings.max_cluster_bias_DUP'
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47 --max_cluster_bias_TRA '$sel_method.adv_settings.max_cluster_bias_TRA'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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48 --diff_ratio_filtering_TRA '$sel_method.adv_settings.diff_ratio_filtering_TRA'
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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49 ]]></command>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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50 <inputs>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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51 <param name="input_sample_file" type="data" format="bam" label="Sample file" help="Sample file in .BAM format." />
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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52 <expand macro="reference_interface" />
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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53 <param name="sample" type="text" value="Sample" label="Sample name/id" help="">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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54 <validator type="length" min="1" message="Please enter a sample name/id"/>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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55 <validator type="regex" message="Please enter a sample name/id">.*[^ ].*</validator>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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56 </param>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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57 <conditional name="sel_method">
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58 <param name="meth_selector" type="select" label="Select the sequencing method of the input file" help="">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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59 <option value="pb_clr" selected="True">PacBio continuous long reads</option>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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60 <option value="pb_ccs">PacBio circular consensus sequencing (HiFi)</option>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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61 <option value="pb_ont">ONT</option>
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62 <option value="other">other method</option>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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63 </param>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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64 <when value="pb_clr">
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65 <section name="adv_settings" title="Advanced settings" expanded="false">
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66 <expand macro="adv_shared_1" />
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67 <expand macro="adv_pb_clr" />
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68 <expand macro="adv_shared_2" />
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69 </section>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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70 </when>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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71 <when value="pb_ccs">
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72 <section name="adv_settings" title="Advanced settings" expanded="false">
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73 <expand macro="adv_shared_1" />
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74 <expand macro="adv_pb_ccs" />
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75 <expand macro="adv_shared_2" />
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76 </section>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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77 </when>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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78 <when value="pb_ont">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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79 <section name="adv_settings" title="Advanced settings" expanded="false">
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80 <expand macro="adv_shared_1" />
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81 <expand macro="adv_ont" />
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82 <expand macro="adv_shared_2" />
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83 </section>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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84 </when>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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85 <when value="other">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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86 <section name="adv_settings" title="Advanced settings" expanded="true">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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87 <expand macro="adv_shared_1" />
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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88 <expand macro="adv_other" />
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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89 <expand macro="adv_shared_2" />
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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90 </section>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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91 </when>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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92 </conditional>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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93 </inputs>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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94 <outputs>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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95 <data name="out_sample" format="vcf" label="${tool.name} on ${on_string}: output" from_work_dir="output.vcf" />
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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96 </outputs>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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97 <tests>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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98 <test expect_num_outputs="1">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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99 <conditional name="reference_source">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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100 <param name="ref_selector" value="history"/>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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101 <param name="ref" ftype="fasta" value="genome.fasta" />
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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102 </conditional>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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103 <param name="seq_method" value="pb_ccs" />
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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104 <param name="input_sample_file" ftype="bam" value="sample.bam" />
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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105 <output name="out_sample">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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106 <assert_contents>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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107 <has_text text="##fileformat=VCFv4.2"/>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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108 <has_text text="##source=cuteSV-1.0.8"/>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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109 </assert_contents>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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110 </output>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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111 </test>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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112 <test expect_num_outputs="1">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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113 <conditional name="reference_source">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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114 <param name="ref_selector" value="cached"/>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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115 <param name="ref" value="test_buildid"/>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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116 </conditional>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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117 <param name="seq_method" value="pb_ccs" />
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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118 <param name="input_sample_file" ftype="bam" value="sample.bam" />
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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119 <output name="out_sample">
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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120 <assert_contents>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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121 <has_text text="##fileformat=VCFv4.2"/>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
iuc
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122 <has_text text="##source=cuteSV-1.0.8"/>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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123 </assert_contents>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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124 </output>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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125 </test>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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126 </tests>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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127 <help><![CDATA[
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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128 cuteSV
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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129 =============
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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130
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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131 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.
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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132
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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133 For more information see the cuteSV documentation_.
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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134
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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135 .. _documentation: https://github.com/tjiangHIT/cuteSV
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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136
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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137 ]]></help>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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138 <citations>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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139 <citation type="doi">10.1186/s13059-020-02107-y</citation>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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140 </citations>
c0f8fe52948e "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cutesv commit abfd3162e28a388d1dedbe55cb8b3567fa79c178"
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141 </tool>