Mercurial > repos > nate > data_manager_hisat2_index_builder

annotate data_manager/hisat2_index_builder.xml @ 2:b3d94db291c1 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
author nate
date Tue, 29 Jul 2025 17:09:29 +0000
parents f7c16185b8e1
children c6a1b04e2f2b
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f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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1 <tool id="hisat2_index_builder_data_manager" name="HISAT2 index" tool_type="manage_data" version="@WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.0">
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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2 <description>builder</description>
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3 <macros>
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4 <token name="@WRAPPER_VERSION@">2.2.1</token>
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b3d94db291c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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5 <token name="@VERSION_SUFFIX@">1</token>
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f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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6 </macros>
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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7 <requirements>
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8 <requirement type="package" version="@WRAPPER_VERSION@">hisat2</requirement>
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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9 </requirements>
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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10 <command detect_errors="exit_code"><![CDATA[
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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11 #set $value = $sequence_id or $all_fasta_source.fields.dbkey
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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12 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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13 #if $advanced.adv_param_select == 'yes' and $advanced.gtf_input:
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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14 ln -s '${advanced.gtf_input}' gtf_file.gtf &&
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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15 hisat2_extract_splice_sites.py gtf_file.gtf > splice_sites.txt &&
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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16 hisat2_extract_exons.py gtf_file.gtf > exon.txt &&
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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17 #end if
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18 #if $advanced.adv_param_select == 'yes' and $advanced.snps:
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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19 ln -s '${advanced.snps}' snps.tabular &&
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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20 #if $advanced.snps.is_of_type('vcf')
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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21 hisat2_extract_snps_haplotypes_VCF.py '${all_fasta_source.fields.path}' snps.tabular extracted &&
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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22 #else
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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23 hisat2_extract_snps_haplotypes_UCSC.py '${all_fasta_source.fields.path}' snps.tabular extracted &&
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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24 #end if
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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25 #end if
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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26
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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27 mkdir -p '${out_file.extra_files_path}' &&
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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28 ln -s '${all_fasta_source.fields.path}' '${out_file.extra_files_path}/${fasta_file_name}' &&
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b3d94db291c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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29 working=$(pwd)` &&
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f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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30 cd '${out_file.extra_files_path}' &&
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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31
2
b3d94db291c1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 5c5d8acf6955dc4f404998ac7929f13363ef2c41
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32 hisat2-build -p "\${GALAXY_SLOTS:-1}"
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f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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33 #if $advanced.adv_param_select == 'yes':
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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34 --noauto
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35 #if $advanced.snps:
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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36 --snp "\${working}/extracted.snp"
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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37 --haplotype "\${working}/extracted.haplotype"
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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38 #end if
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39 #if $advanced.gtf_input:
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40 --ss "\${working}/splice_sites.txt"
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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41 --exon "\${working}/exon.txt"
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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42 #end if
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43 --bmax $advanced.bmax
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44 --bmaxdivn $advanced.bmaxdivn
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45 --dcv $advanced.dcv
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46 --offrate $advanced.offrate
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47 #end if
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48 '${fasta_file_name}' '${value}' &&
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49 rm '${out_file.extra_files_path}/${fasta_file_name}' &&
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50
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51 cp '$dmjson' '$out_file'
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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52 ]]>
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53 </command>
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54 <configfiles>
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55 <configfile name="dmjson"><![CDATA[#slurp
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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56 #set $fasta_file_name = str($all_fasta_source.fields.path).split('/')[-1]
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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57 #set $value = $sequence_id or $all_fasta_source.fields.dbkey
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58 #set $name = $sequence_name or $all_fasta_source.fields.name
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59 {
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60 "data_tables":{
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61 "hisat2_indexes":[
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62 {
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63 "value": "${value}",
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64 "dbkey": "${all_fasta_source.fields.dbkey}",
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
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65 "name": "${name}",
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66 "path": "${value}"
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67 }
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68 ]
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69 }
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70 }
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71 ]]></configfile>
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72 </configfiles>
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73 <inputs>
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74 <param label="Source FASTA Sequence" name="all_fasta_source" type="select">
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75 <options from_data_table="all_fasta" />
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76 </param>
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77 <conditional name="advanced" label="Advanced parameters">
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78 <param name="adv_param_select" type="select" label="Advanced parameters">
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79 <option value="no">Use defaults</option>
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80 <option value="yes">Fine-tune indexing parameters</option>
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81 </param>
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82 <when value="no" />
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83 <when value="yes">
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84 <param argument="--bmax" type="integer" value="4" label="Maximum number of suffixes allowed in a block" />
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85 <param argument="--bmaxdivn" type="integer" value="4" label="Maximum number of suffixes allowed in a block, expressed as a fraction of the length of the reference" />
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86 <param argument="--dcv" type="integer" min="2" max="4096" value="1024" label="Period for the difference-cover sample" help="A larger period yields less memory overhead, but may make suffix sorting slower, especially if repeats are present. Must be a power of 2 no greater than 4096" />
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87 <param argument="--offrate" type="integer" value="4" label="Mark rows in the Burrows-Wheeler transform" help="To map alignments back to positions on the reference sequences, it's necessary to annotate (&quot;mark&quot;) some or all of the Burrows-Wheeler rows with their corresponding location on the genome. This parameter governs how many rows get marked: the indexer will mark every 2^&lt;int&gt; rows. Marking more rows makes reference-position lookups faster, but requires more memory to hold the annotations at runtime. The default is 4 (every 16th row is marked; for human genome, annotations occupy about 680 megabytes)" />
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88 <param name="snps" type="data" format="tabular,vcf" optional="true" label="Provide a list of SNPs in the UCSC dbSNP or VCF format" help="If you include SNPs or splice sites and exons, building an index on the human genome will consume up to 200GB RAM as index building involves a graph construction" />
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89 <param name="gtf_input" type="data" format="gtf" optional="true" label="Provide a GTF file for HISAT2 to extract splice sites from" help="If you include SNPs or splice sites and exons, building an index on the human genome will consume up to 200GB RAM as index building involves a graph construction" />
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90 </when>
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91 </conditional>
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92 <param name="sequence_name" type="text" value="" label="Name of sequence" />
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93 <param name="sequence_id" type="text" value="" label="ID for sequence" />
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94 </inputs>
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95 <outputs>
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96 <data name="out_file" format="data_manager_json" />
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97 </outputs>
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98 <tests>
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99 <test>
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100 <param name="all_fasta_source" value="phiX174"/>
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101 <output name="out_file" file="hisat2_data_manager.1.json"/>
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102 </test>
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103 <test>
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104 <param name="all_fasta_source" value="phiX174"/>
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105 <param name="sequence_name" value="Galeocerdo cuvier"/>
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106 <param name="sequence_id" value="tigHai1"/>
2
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107 <param name="advanced|adv_param_select" value="yes"/>
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108 <param name="advanced|bmax" value="3"/>
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109 <param name="advanced|bmaxdivn" value="3"/>
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110 <param name="advanced|dcv" value="4"/>
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111 <param name="advanced|offrate" value="5"/>
0
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112 <output name="out_file" file="hisat2_data_manager.2.json"/>
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113 </test>
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114 </tests>
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115 <help>
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116 <![CDATA[
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117 .. class:: infomark
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118
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119 **Notice:** If you leave name, description, or id blank, it will be generated automatically.
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120
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121 What is HISAT2?
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122 ---------------
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123
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124 `HISAT <http://ccb.jhu.edu/software/hisat>`__ is a fast and sensitive alignment
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125 program for mapping next-generation sequencing reads (both DNA and RNA) against
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126 the general human population (as well as against a single reference genome).
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127 Based on an extension of BWT for graphs (`BWT <http://dl.acm.org/citation.cfm?id=2674828>`__)
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128 we designed and implemented a graph FM index (GFM), an original approach and
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129 its first implementation to the best of our knowledge. In addition to using one
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130 global GFM index that represents the general population, HISAT2 uses a large set
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131 of small GFM indexes that collectively cover the whole genome (each index
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132 representing a genomic region of 56 Kbp, with 55,000 indexes needed to cover
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133 the human population). These small indexes (called local indexes), combined
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134 with several alignment strategies, enable rapid and accurate alignment of
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135 sequencing reads. This new indexing scheme is called a Hierarchical Graph
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136 FM index (HGFM). In addition to spliced alignment, HISAT handles reads
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137 involving indels and supports a paired-end alignment mode. Multiple processors
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138 can be used simultaneously to achieve greater alignment speed. HISAT outputs
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139 alignments in `SAM <http://samtools.sourceforge.net/SAM1.pdf>`__ format, enabling
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140 interoperation with a large number of other tools (e.g. `SAMtools <http://samtools.sourceforge.net>`__,
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141 `GATK <http://www.broadinstitute.org/gsa/wiki/index.php/The_Genome_Analysis_Toolkit>`__)
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142 that use SAM. HISAT is distributed under the `GPLv3 license <http://www.gnu.org/licenses/gpl-3.0.html>`__,
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143 and it runs on the command line under Linux, Mac OS X and Windows.
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144 ]]>
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145 </help>
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146 <citations>
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147 <citation type="doi">10.1038/nmeth.3317</citation>
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148 </citations>
f7c16185b8e1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_hisat2_index_builder commit 36a598c1014c3fa9696c4bdbf13d98a9e1e528c9
nate
parents:
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149 </tool>