Mercurial > repos > iuc > tbprofiler

annotate tb_profiler_profile.xml @ 16:2c68b0c38785 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit b6d3c87b5000ddfef726e72ba00b0b3bf2978acd
author iuc
date Sun, 22 Jan 2023 10:48:05 +0000
parents 45083d070fb8
children d03af1c7002c
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1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0" profile="20.09">
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2 <description>Infer strain types and drug resistance markers from sequences</description>
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3 <macros>
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4 <token name="@TOOL_VERSION@">4.4.1</token>
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5 </macros>
0
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6 <requirements>
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7 <requirement type="package" version="@TOOL_VERSION@">tb-profiler</requirement>
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8 </requirements>
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9 <command detect_errors="exit_code"><![CDATA[
1
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10 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
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11 #if str($fastq_or_bam.input_select.value) == "paired_fastq"
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12 #set r1_ext = $fastq_or_bam.read1.extension
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13 #set r2_ext = $fastq_or_bam.read2.extension
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14 ln -s '$fastq_or_bam.read1' fastq_r1.'$r1_ext' &&
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15 ln -s '$fastq_or_bam.read2' fastq_r2.'$r2_ext' &&
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16 #else if str($fastq_or_bam.input_select.value) == "single_fastq"
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17 #set r1_ext = $fastq_or_bam.fastq.extension
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18 ln -s '$fastq_or_bam.fastq' fastq_r1.'$r1_ext' &&
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19 #else if str($fastq_or_bam.input_select.value) == "paired_collection_fastq"
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20 #set r1_ext = $fastq_or_bam.fastq_collection.forward.extension
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21 #set r2_ext = $fastq_or_bam.fastq_collection.reverse.extension
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22 ln -s '$fastq_or_bam.fastq_collection.forward' fastq_r1.'$r1_ext' &&
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23 ln -s '$fastq_or_bam.fastq_collection.reverse' fastq_r2.'$r2_ext' &&
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24 #end if
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25 #else if str($fastq_or_bam.input_select.value) == "bam"
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26 ln -s '$fastq_or_bam.bam_input' input.bam &&
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27 #end if
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28
0
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29 tb-profiler profile
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30 --platform '${platform.value}'
1
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31 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
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32 -1 fastq_r1.'$r1_ext'
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33 #end if
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34 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq")
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35 -2 fastq_r2.'$r1_ext'
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36 #else if str($fastq_or_bam.input_select.value) == "bam"
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37 --bam input.bam
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38 #end if
0
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39
1
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40 --threads "\${GALAXY_SLOTS:-1}"
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41 #if $advanced.options == 'yes'
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42 --mapper '${advanced.mapper}'
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43 --caller '${advanced.caller}'
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44 --min_depth '${advanced.min_depth}'
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45 --af '${advanced.min_allele_freq}'
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46 --reporting_af '${advanced.min_allele_freq_reporting}'
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47 #end if
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48
1
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49 #if $output_format == "pdf"
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50 --pdf
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51 #else if $output_format == "txt"
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52 --txt
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53 #end if
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54 && mv results/tbprofiler.results.json $results_json
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55 #if str($fastq_or_bam.input_select) != "bam"
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56 && mv bam/tbprofiler.bam '${output_bam}'
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57 #end if
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58 && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.csq.vcf.gz
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59 #if $output_format == "pdf"
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60 && mv results/tbprofiler.results.pdf '${output_pdf}'
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61 #else if $output_format == "txt"
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62 && mv results/tbprofiler.results.txt '${output_txt}'
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63 #end if
0
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64
2
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65 ]]> </command>
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66 <inputs>
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67 <param name="platform" type="select" label="Platform">
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68 <option value="illumina" selected="true">Illumina</option>
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69 <option value="nanopore">Nanopore</option>
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70 <option value="pacbio">PacBio</option>
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71 </param>
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72 <conditional name="fastq_or_bam">
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73 <param name="input_select" type="select" label="Input File Type">
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74 <option value="paired_fastq">Paired Fastq</option>
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75 <option value="paired_collection_fastq">Paired Collection Fastq</option>
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76 <option value="single_fastq">Single Fastq</option>
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77 <option value="bam">BAM</option>
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78 </param>
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79 <when value="paired_fastq">
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80 <param name="read1" type="data" format="fastq" label="Read1" help="First read file (default: None)"/>
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81 <param name="read2" type="data" format="fastq" optional="true" label="Read2" help="Second read file (default: None)"/>
1
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82 </when>
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83 <when value="paired_collection_fastq">
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84 <param label="Reads (collection)" name="fastq_collection" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
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parents: 0
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85 </when>
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86 <when value="single_fastq">
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87 <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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88 </when>
0
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89 <when value="bam">
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90 <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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91 </when>
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92 </conditional>
1
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93 <param name="output_format" label="Output format" type="select">
9
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94 <option value="txt" selected="true">Text</option>
1
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95 <option value="pdf">PDF</option>
0
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96 </param>
1
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97 <conditional name="advanced">
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98 <param label="Select advanced options" type="select" name="options">
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99 <option value="yes">Yes</option>
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100 <option value="no" selected="true">No</option>
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101 </param>
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102 <when value="no">
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103 </when>
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104 <when value="yes">
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105 <param argument="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
1
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106 <option value="bwa" selected="true">bwa</option>
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107 <option value="minimap2">minimap2</option>
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108 <option value="bowtie2">bowtie2</option>
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109 <option value="bwa-mem2">bwa-mem2</option>
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110 </param>
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111 <param argument="caller" label="Variant caller" help="Variant calling tool to use" type="select">
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112 <option value="freebayes" selected="true">freebayes</option>
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113 <option value="bcftools">bcftools</option>
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114 <option value="gatk">gatk</option>
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115 <option value="pilon">pilon</option>
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116 <option value="lofreq">lofreq</option>
1
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117 </param>
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118 <param name="min_depth" label="Min Depth" type="integer" value="10" help="Minimum depth required to call variant. Bases with depth below this cutoff will be marked as missing (default: 10)"/>
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119 <param name="min_allele_freq" argument="--af" type="float" value="0.1" label="Minimum allele frequency to call variants" help=" Minimum allele frequency to call variants (default: 0.1)" />
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120 <param name="min_allele_freq_reporting" argument="--reporting_af" value="0.1" label="Reporting Minimum allele frequency to call variants" type="float" help=" Minimum allele frequency to call variants (default: 0.1)"/>
1
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121 </when>
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122 </conditional>
0
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123 </inputs>
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124 <outputs>
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125 <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
1
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126 <data format="vcf" name="output_vcf" label="${tool.name} VCF on ${on_string}" />
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127 <data format="bam" name="output_bam" label="${tool.name} BAM on ${on_string}">
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128 <filter>fastq_or_bam['input_select'] != 'bam'</filter>
0
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129 </data>
1
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130 <data format="pdf" name="output_pdf" label="${tool.name} PDF report on ${on_string}">
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131 <filter>output_format == 'pdf'</filter>
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132 </data>
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133 <data format="txt" name="output_txt" label="${tool.name} report on ${on_string}">
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134 <filter>output_format == 'txt'</filter>
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135 </data>
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136
0
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137 </outputs>
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138 <tests>
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139 <test expect_num_outputs="4">
1
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140 <param name="input_select" value="single_fastq"/>
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141 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
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142 <param name="output_format" value="txt" />
5
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143 <param name="platform" value="illumina" />
1
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144 <param name="options" value="no" />
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145 <output name="output_txt">
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146 <assert_contents>
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147 <has_line line="Drug-resistance: RR-TB" />
15
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148 <has_line line="lineage2.2.2&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
2
49b819f88c2b planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit da74c7f8419319266b84dcac128ad84d8fc2216d
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parents: 1
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149 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
15
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150 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
1
5182e1a99313 planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 761cc6083b4db7e69ddf03033bc8659b08e16f74
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151 </assert_contents>
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152 </output>
0
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153 </test>
9
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154 <test expect_num_outputs="3">
1
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parents: 0
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155 <param name="input_select" value="bam"/>
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156 <param name="bam_input" ftype="bam" value="rif_resistant.bam" />
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157 <param name="output_format" value="txt" />
5
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parents: 4
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158 <param name="platform" value="illumina" />
1
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159 <param name="options" value="no" />
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160 <output name="output_txt">
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161 <assert_contents>
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162 <has_line line="Drug-resistance: RR-TB" />
15
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163 <has_line line="lineage2.2.2&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
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164 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
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165 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
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166 </assert_contents>
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167 </output>
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168 </test>
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169 <test expect_num_outputs="4">
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170 <param name="input_select" value="single_fastq"/>
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171 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
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172 <param name="output_format" value="txt" />
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173 <param name="platform" value="illumina" />
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174 <param name="options" value="yes" />
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175 <param name="min_allele_freq" value="0.25" />
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176 <param name="min_allele_freq_reporting" value="0.33" />
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177 <output name="output_txt">
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178 <assert_contents>
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179 <has_line line="Drug-resistance: RR-TB" />
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180 <has_line line="lineage2.2.2&#009;1.000&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
7
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181 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
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182 <has_line line="761110&#009;Rv0667&#009;rpoB&#009;missense_variant&#009;p.Asp435Val&#009;1.000&#009;rifampicin&#009;type=who_confidence|drug=rifampicin|who_confidence=Assoc w R" />
7
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183 </assert_contents>
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184 </output>
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185 </test>
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186 </tests>
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187 <help><![CDATA[
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188 Summary
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189 =======
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190
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191 The pipeline aligns reads to the H37Rv reference using BWA, bowtie2 or minimap2 and then calls variants
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192 (using bcftools, GATK4 or freebayes). These variants are then compared to a drug-resistance database.
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193 TB-Profiler also predicts the number of reads supporting drug resistance variants as an insight into
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194 hetero-resistance (not applicable for MinION data).
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195
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196 Produces a JSON output file by default.
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197
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198 ]]> </help>
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199 <citations>
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200 <citation type="doi">10.1186/s13073-019-0650-x</citation>
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201 </citations>
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202 </tool>