Mercurial > repos > iuc > tbprofiler

annotate tb_profiler_profile.xml @ 18:4839e590cb26 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 74ef4277d954bbbb0acd47ae6ef2d323485d5bf1
author iuc
date Thu, 30 May 2024 11:31:53 +0000
parents d03af1c7002c
children 51dd22484644
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1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="23.2" license="AGPL-3.0-or-later">
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2 <description>Infer strain types and drug resistance markers from sequences</description>
3
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3 <macros>
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4 <token name="@TOOL_VERSION@">6.2.1</token>
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5 </macros>
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6 <xrefs>
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7 <xref type="bio.tools">tb-profiler</xref>
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8 </xrefs>
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9 <requirements>
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10 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
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11 </requirements>
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12 <command detect_errors="exit_code"><![CDATA[
1
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13 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
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14 #if str($fastq_or_bam.input_select.value) == "paired_fastq"
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15 #set r1_ext = $fastq_or_bam.read1.extension
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16 #set r2_ext = $fastq_or_bam.read2.extension
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17 ln -s '$fastq_or_bam.read1' fastq_r1.'$r1_ext' &&
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18 ln -s '$fastq_or_bam.read2' fastq_r2.'$r2_ext' &&
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19 #else if str($fastq_or_bam.input_select.value) == "single_fastq"
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20 #set r1_ext = $fastq_or_bam.fastq.extension
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21 ln -s '$fastq_or_bam.fastq' fastq_r1.'$r1_ext' &&
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22 #else if str($fastq_or_bam.input_select.value) == "paired_collection_fastq"
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23 #set r1_ext = $fastq_or_bam.fastq_collection.forward.extension
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24 #set r2_ext = $fastq_or_bam.fastq_collection.reverse.extension
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25 ln -s '$fastq_or_bam.fastq_collection.forward' fastq_r1.'$r1_ext' &&
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26 ln -s '$fastq_or_bam.fastq_collection.reverse' fastq_r2.'$r2_ext' &&
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27 #end if
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28 #else if str($fastq_or_bam.input_select.value) == "bam"
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29 ln -s '$fastq_or_bam.bam_input' input.bam &&
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30 #end if
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31
0
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32 tb-profiler profile
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33 --platform '${platform.value}'
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34 ${spoligotype}
1
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35 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
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36 -1 fastq_r1.'$r1_ext'
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37 #end if
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38 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq")
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39 -2 fastq_r2.'$r1_ext'
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40 #else if str($fastq_or_bam.input_select.value) == "bam"
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41 --bam input.bam
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42 #end if
0
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43
1
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44 --threads "\${GALAXY_SLOTS:-1}"
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45 #if $advanced.options == 'yes'
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46 --mapper '${advanced.mapper}'
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47 --caller '${advanced.caller}'
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48 --depth '${advanced.vf.min_depth_hard},${advanced.vf.min_depth_soft}'
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49 --af '${advanced.vf.min_af_hard},${advanced.vf.min_af_soft}'
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50 --strand '${advanced.vf.min_read_hard},${advanced.vf.min_read_soft}'
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51 --sv-depth '${advanced.vf.min_sv_depth_hard},${advanced.vf.min_sv_depth_soft}'
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52 --sv-af '${advanced.vf.min_sv_af_hard},${advanced.vf.min_sv_af_soft}'
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53 --sv-len '${advanced.vf.max_sv_len_hard},${advanced.vf.max_sv_len_soft}'
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54 ${advanced.suspect}
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55 ${advanced.no_trim}
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56 ${advanced.no_coverage_qc}
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57 ${advanced.no_samclip}
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58 ${advanced.no_delly}
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59 #end if
0
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60
1
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61 #if $output_format == "pdf"
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62 --pdf
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63 #else if $output_format == "txt"
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64 --txt
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65 #end if
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66 && mv results/tbprofiler.results.json $results_json
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67 #if str($fastq_or_bam.input_select) != "bam"
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68 && mv bam/tbprofiler.bam '${output_bam}'
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69 #end if
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70 && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.vcf.gz
1
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71 #if $output_format == "pdf"
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72 && mv results/tbprofiler.results.pdf '${output_pdf}'
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73 #else if $output_format == "txt"
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74 && mv results/tbprofiler.results.txt '${output_txt}'
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75 #end if
0
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76
2
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77 ]]> </command>
0
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78 <inputs>
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79 <param name="platform" type="select" label="Platform">
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80 <option value="illumina" selected="true">Illumina</option>
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81 <option value="nanopore">Nanopore</option>
15
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82 <option value="pacbio">PacBio</option>
0
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83 </param>
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84 <conditional name="fastq_or_bam">
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85 <param name="input_select" type="select" label="Input File Type">
1
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parents: 0
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86 <option value="paired_fastq">Paired Fastq</option>
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87 <option value="paired_collection_fastq">Paired Collection Fastq</option>
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parents: 0
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88 <option value="single_fastq">Single Fastq</option>
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89 <option value="bam">BAM</option>
0
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90 </param>
1
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parents: 0
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91 <when value="paired_fastq">
0
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92 <param name="read1" type="data" format="fastq" label="Read1" help="First read file (default: None)"/>
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93 <param name="read2" type="data" format="fastq" optional="true" label="Read2" help="Second read file (default: None)"/>
1
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parents: 0
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94 </when>
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95 <when value="paired_collection_fastq">
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96 <param label="Reads (collection)" name="fastq_collection" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
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97 </when>
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98 <when value="single_fastq">
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parents: 0
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99 <param label="Reads" name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
2
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parents: 1
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100 </when>
0
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101 <when value="bam">
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102 <param name="bam_input" type="data" format="bam" label="Bam" help="Warning!!!: The BAM files must have been created using the ensembl version of the genome."/>
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103 </when>
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104 </conditional>
18
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105 <param argument="--spoligotype" type="boolean" label="Perform in-silico spoligotyping" checked="false" truevalue="--spoligotype" falsevalue=""
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106 help="Uses spacers of CRISPR region to call a spoligotype."/>
1
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107 <param name="output_format" label="Output format" type="select">
9
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108 <option value="txt" selected="true">Text</option>
1
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109 <option value="pdf">PDF</option>
0
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110 </param>
1
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111 <conditional name="advanced">
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112 <param label="Select advanced options" type="select" name="options">
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113 <option value="yes">Yes</option>
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114 <option value="no" selected="true">No</option>
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115 </param>
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116 <when value="no">
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117 </when>
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118 <when value="yes">
14
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119 <param argument="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
1
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120 <option value="bwa" selected="true">bwa</option>
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121 <option value="minimap2">minimap2</option>
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122 <option value="bowtie2">bowtie2</option>
14
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123 <option value="bwa-mem2">bwa-mem2</option>
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124 </param>
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125 <param argument="caller" label="Variant caller" help="Variant calling tool to use" type="select">
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126 <option value="freebayes" selected="true">freebayes</option>
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127 <option value="bcftools">bcftools</option>
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128 <option value="gatk">gatk</option>
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129 <option value="pilon">pilon</option>
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130 <option value="lofreq">lofreq</option>
1
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131 </param>
18
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132 <section name="vf" title="Variant Filters">
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133 <param name="min_depth_hard" argument="--depth" label="Min Depth (hard cutoff)" type="integer" value="0" min="0"
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134 help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 0)"/>
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135 <param name="min_depth_soft" argument="--depth" label="Min Depth (soft cutoff)" type="integer" value="10" min="0"
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136 help="Minimum depth required to call variant. Variants at positions lower than this depth and above the hard cutoff will be marked as QC fail (default: 10)"/>
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137 <param name="min_af_hard" argument="--af" type="float" value="0" label="Minimum allele frequency to call variants (hard cutoff)" min="0.0" max="1.0"
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138 help="Minimum allele frequency to call variants (default: 0)" />
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139 <param name="min_af_soft" argument="--af" type="float" value="0.1" label="Minimum allele frequency to call variants (soft cutoff)" min="0.0" max="1.0"
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140 help="Variants with an allele frequency lower than this (and higher than the hard cutoff) will be marked as QC fail (default 0.1)" />
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141 <param name="min_read_hard" argument="--strand" type="integer" value="0" label="Mininum read number per strand (hard cutoff)" min="0"
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142 help="Minimum read number per strand to call variants (default: 0)" />
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143 <param name="min_read_soft" argument="--strand" type="integer" value="3" label="Mininum read number per strand (soft cutoff)" min="0"
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144 help="Minimum read number per strand to report variants (default: 3). Variants with number of reads on each strand below this (and above the hard cutoff) will be marked as QC fail" />
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145 <param name="min_sv_depth_hard" argument="--sv-depth" type="integer" value="0" label="Min Depth for SV (hard cutoff)" min="0"
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146 help="Minimum depth required to call structural variants (default: 0)" />
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147 <param name="min_sv_depth_soft" argument="--sv-depth" type="integer" value="10" label="Min Depth for SV (soft cutoff)" min="0"
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148 help="Minimum depth required to call structural variants. Variants at positions lower than this depth and above the hard cutoff will be marked as QC fail" />
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149 <param name="min_sv_af_hard" argument="--sv-af" type="float" value="0.5" label="Min SV allele frequency (hard cutoff)" min="0.0" max="1.0"
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150 help="Minimum allele frequency to call structural variants (default: 0.5)" />
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151 <param name="min_sv_af_soft" argument="--sv-af" type="float" value="0.9" label="Min SV allele frequency (soft cutoff)" min="0.0" max="1.0"
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152 help="Variants with an allele frequency lower than this (and higher than the hard cutoff) will be marked as QC fail (default 0.9)" />
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153 <param name="max_sv_len_hard" argument="--sv-len" type="integer" value="100000" label="Max SV length (hard cutoff)" min="0"
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154 help="Maximum length (length) of structural variants to call (default: 100000)" />
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155 <param name="max_sv_len_soft" argument="--sv-len" type="integer" value="50000" label="Max SV length (soft cutoff)" min="0"
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156 help="Structural variants with length higher than this (and lower than the hard cutoff) will be marked as QC fail (default: 50000)" />
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157 </section>
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158 <param argument="--suspect" label="Use ML predictions of resistance from the SUSPECT tool suite" type="boolean" checked="False" truevalue="--suspect" falsevalue=""
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159 help="The SUSPECT tools offer ML-based predictions of RIF, PZA and BDQ resistance. Note that this uses a web service thus requires an Internet connection."/>
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160 <param argument="--no_trim" label="Do not trim reads using trimmomatic" checked="false" type="boolean" truevalue="--no_trim" falsevalue="" />
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161 <param argument="--no_coverage_qc" label="Don't collect flagstats" type="boolean" truevalue="--no_coverage_qc" falsevalue="" />
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162 <param argument="--no_samclip" label="Don't removed clipped reads from variant calling" type="boolean" truevalue="--no_samclip" falsevalue="" />
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163 <param argument="--no_delly" label="Don't run delly for SV calling" type="boolean" truevalue="--no_delly" falsevalue="" />
1
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164 </when>
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165 </conditional>
0
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166 </inputs>
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167 <outputs>
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168 <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
1
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169 <data format="vcf" name="output_vcf" label="${tool.name} VCF on ${on_string}" />
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170 <data format="bam" name="output_bam" label="${tool.name} BAM on ${on_string}">
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171 <filter>fastq_or_bam['input_select'] != 'bam'</filter>
0
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172 </data>
1
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173 <data format="pdf" name="output_pdf" label="${tool.name} PDF report on ${on_string}">
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174 <filter>output_format == 'pdf'</filter>
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175 </data>
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176 <data format="txt" name="output_txt" label="${tool.name} report on ${on_string}">
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177 <filter>output_format == 'txt'</filter>
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178 </data>
0
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179 </outputs>
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180 <tests>
9
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181 <test expect_num_outputs="4">
1
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182 <param name="input_select" value="single_fastq"/>
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183 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
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184 <param name="output_format" value="txt" />
5
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185 <param name="platform" value="illumina" />
1
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186 <param name="options" value="no" />
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187 <output name="output_txt">
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188 <assert_contents>
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189 <has_line line="Drug-resistance: RR-TB" />
18
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190 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
2
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parents: 1
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191 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
18
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192 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
1
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193 </assert_contents>
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194 </output>
0
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195 </test>
9
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196 <test expect_num_outputs="3">
1
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197 <param name="input_select" value="bam"/>
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198 <param name="bam_input" ftype="bam" value="rif_resistant.bam" />
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199 <param name="output_format" value="txt" />
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200 <param name="platform" value="illumina" />
1
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201 <param name="options" value="no" />
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202 <output name="output_txt">
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203 <assert_contents>
14
ac8250086ac3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 7598f8402d6adaab0e7c9a3cd426914f700be336"
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204 <has_line line="Drug-resistance: RR-TB" />
18
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parents: 17
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205 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
2
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
iuc
parents: 1
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206 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
18
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207 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
1
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parents: 0
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208 </assert_contents>
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209 </output>
0
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210 </test>
9
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211 <test expect_num_outputs="4">
7
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212 <param name="input_select" value="single_fastq"/>
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213 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
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214 <param name="output_format" value="txt" />
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215 <param name="platform" value="illumina" />
18
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diff changeset
216 <conditional name="advanced">
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217 <param name="options" value="yes" />
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218 <section name="vf">
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219 <param name="min_depth_hard" value="40" />
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220 <param name="min_depth_soft" value="50" />
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221 </section>
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222 </conditional>
7
200c378d85f3 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 53f6ccebd38e89bb2e67b2eec3aee30b4e141b5b"
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223 <output name="output_txt">
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224 <assert_contents>
18
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225 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;RD105;RD207" />
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226 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
4839e590cb26 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 74ef4277d954bbbb0acd47ae6ef2d323485d5bf1
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227 </assert_contents>
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228 </output>
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229 <output name="results_json">
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230 <assert_contents>
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231 <has_text text='"filter": "soft_fail",' />
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232 </assert_contents>
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233 </output>
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234 </test>
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235 <test expect_num_outputs="4">
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236 <param name="input_select" value="single_fastq"/>
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diff changeset
237 <param name="fastq" ftype="fastq.gz" value="rpoB_and_crispr.fastq.gz" />
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238 <param name="output_format" value="txt" />
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239 <param name="platform" value="illumina" />
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240 <param name="spoligotype" value="true" />
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241 <param name="options" value="no" />
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242 <output name="output_txt">
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243 <assert_contents>
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244 <has_line line="Octal: 000000000000771" />
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245 <has_line line="Drug-resistance: RR-TB" />
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246 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
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247 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;Assoc w R" />
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248 </assert_contents>
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249 </output>
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250 </test>
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251 </tests>
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252 <help><![CDATA[
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253 Summary
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254 =======
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255
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256 The pipeline aligns reads to the H37Rv reference using BWA, bowtie2 or minimap2 and then calls variants
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257 (using bcftools, GATK4 or freebayes). These variants are then compared to a drug-resistance database.
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258 TB-Profiler also predicts the number of reads supporting drug resistance variants as an insight into
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259 hetero-resistance (not applicable for MinION data).
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260
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261 Produces a JSON output file by default.
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262
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263 In the Advanced options, you can select the mapper and variant caller to use, as well as set a number of filtering parameters.
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264 Each of these typically has a "hard" and a "soft" cutoff. If a variant value is below the "hard" cutoff it is discarded, if
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265 it is between the "hard" and "soft" values it is removed from the final predictions but added to the "qc_fail_variants" section
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266 of the output.
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267
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268 One of the advanced options is to use the SUSPECT tool suite to predict resistance to `rifampicin (RIF)`_, `pyrazinamide (PZA)`_
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269 and `bedaquiline (BDQ)`_.
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270
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271 .. _rifampicin (RIF): https://www.nature.com/articles/s41598-020-74648-y
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272 .. _pyrazinamide (PZA): https://www.nature.com/articles/s41598-020-58635-x
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273 .. _bedaquiline (BDQ): https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0217169
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274 ]]> </help>
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275 <citations>
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276 <citation type="doi">10.1186/s13073-019-0650-x</citation>
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277 </citations>
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278 </tool>