Mercurial > repos > iuc > tbprofiler

annotate tb_profiler_profile.xml @ 6:f7f32674f751 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 693ca73048b8f27e54c0659ffbb3d04e2ce9873a"
author iuc
date Wed, 22 Jan 2020 14:54:08 -0500
parents 4272bd430a01
children 200c378d85f3
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19793eecc9f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"
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1 <tool id="tb_profiler_profile" name="TB-Profiler Profile" version="@TOOL_VERSION@+galaxy0">
2
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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 <import>macros.xml</import>
19793eecc9f0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit 5679ad1f1d5cac6c6168ad91dd4ca3616d22ca35"
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5 </macros>
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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 '$fastq_or_bam.bam_input' input.bam &&
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27 #end if
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28
0
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29 tb-profiler profile
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31 --platform '${platform.value}'
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32
1
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33 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq", "single_fastq")
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34 -1 fastq_r1.'$r1_ext'
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35 #end if
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36 #if str($fastq_or_bam.input_select.value) in ("paired_fastq", "paired_collection_fastq")
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37 -2 fastq_r2.'$r1_ext'
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38 #else if str($fastq_or_bam.input_select.value) == "bam"
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39 --bam input.bam
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40 #end if
0
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41
1
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42 --threads "\${GALAXY_SLOTS:-1}"
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43 #if $advanced.options == 'yes'
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44 '${advanced.call_whole_genome}'
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45 --call_method '${advanced.call_method}'
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46 --min_gene_frac '${advanced.min_gene_frac}'
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47 --mapper '${advanced.mapper}'
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48 --min_depth '${advanced.min_depth}'
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49 --af '${min_allel_freq}'
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50 --reporting_af '${min_allel_freq_reporting}'
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51 #end if
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52
1
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53 #if $output_format == "pdf"
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54 --pdf
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55 #else if $output_format == "txt"
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56 --txt
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57 #end if
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58 && mv results/tbprofiler.results.json $results_json
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59 #if str($fastq_or_bam.input_select) != "bam"
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60 && mv bam/tbprofiler.bam '${output_bam}'
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61 #end if
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62 && bcftools view -Ov -o'${output_vcf}' vcf/tbprofiler.targets.csq.vcf.gz
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63 #if $output_format == "pdf"
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64 && mv results/tbprofiler.results.pdf '${output_pdf}'
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65 #else if $output_format == "txt"
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66 && mv results/tbprofiler.results.txt '${output_txt}'
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67 #end if
0
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68
2
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69 ]]> </command>
0
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70 <inputs>
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71 <param name="platform" type="select" label="Platform">
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72 <option value="illumina" selected="true">Illumina</option>
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73 <option value="nanopore">Nanopore</option>
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74 </param>
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75 <conditional name="fastq_or_bam">
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76 <param name="input_select" type="select" label="Input File Type">
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77 <option value="paired_fastq">Paired Fastq</option>
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78 <option value="paired_collection_fastq">Paired Collection Fastq</option>
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79 <option value="single_fastq">Single Fastq</option>
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80 <option value="bam">BAM</option>
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81 </param>
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82 <when value="paired_fastq">
0
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83 <param name="read1" type="data" format="fastq" label="Read1" help="First read file (default: None)"/>
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84 <param name="read2" type="data" format="fastq" optional="true" label="Read2" help="Second read file (default: None)"/>
1
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85 </when>
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86 <when value="paired_collection_fastq">
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87 <param label="Reads (collection)" name="fastq_collection" type="data_collection" collection_type="paired" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
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88 </when>
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89 <when value="single_fastq">
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90 <param label="Reads" name="fastq" type="data" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" />
2
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91 </when>
0
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92 <when value="bam">
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93 <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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94 </when>
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95 </conditional>
1
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96 <param name="output_format" label="Output format" type="select">
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97 <option value="txt">Text</option>
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98 <option value="pdf">PDF</option>
0
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99 </param>
1
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100 <conditional name="advanced">
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101 <param label="Select advanced options" type="select" name="options">
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102 <option value="yes">Yes</option>
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103 <option value="no" selected="true">No</option>
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104 </param>
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105 <when value="no">
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106 </when>
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107 <when value="yes">
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108 <param label="Quality required for calls to be accepted" type="select" argument="--call_method">
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109 <option value="low" selected="true">Low</option>
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110 <option value="high">High</option>
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111 <option value="optimise">Optimise</option>
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112 </param>
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113 <param label="Call variants on the whole genome" type="boolean" argument="--call_whole_genome"
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114 truevalue="--call_whole_genome" falsevalue="" help="Call variants on whole genome (Useful if you need to use whole genome variants later)" />
2
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115 <param label="Minimum coverage fraction to infer deletion" type="float" help="Used to infer a deletion if the fraction of a gene covered falls below this value." argument="--min_gene_frac" value="0.9" />
1
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116
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117 <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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118 <param name="mapper" label="Mapper" type="select" help="Mapping tools to use (default: bwa)">
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119 <option value="bwa" selected="true">bwa</option>
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120 <option value="minimap2">minimap2</option>
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121 <option value="bowtie2">bowtie2</option>
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122 </param>
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123 <param name="min_gene_frac" label="Minimum Gene Fraction" type="float" value="0.9" help="Used to infer a deletion if the fraction of a gene covered falls below this value. Also used to see if sample is high quality to continue by checking the fraction for rpoB (where deletion should not occur). (default: 0.9)" />
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124 <param name="min_allel_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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125 <param name="min_allel_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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126 </when>
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127 </conditional>
0
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128 </inputs>
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129 <outputs>
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130 <data name="results_json" format="json" from_work_dir="results/tbprofiler.results.json" label="${tool.name} on ${on_string}: Results.json"/>
1
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131 <data format="vcf" name="output_vcf" label="${tool.name} VCF on ${on_string}" />
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132 <data format="bam" name="output_bam" label="${tool.name} BAM on ${on_string}">
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133 <filter>fastq_or_bam['input_select'] != 'bam'</filter>
0
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134 </data>
1
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135 <data format="pdf" name="output_pdf" label="${tool.name} PDF report on ${on_string}">
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136 <filter>output_format == 'pdf'</filter>
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137 </data>
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138 <data format="txt" name="output_txt" label="${tool.name} report on ${on_string}">
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139 <filter>output_format == 'txt'</filter>
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140 </data>
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141
0
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142 </outputs>
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143 <tests>
1
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144 <test>
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145 <param name="input_select" value="single_fastq"/>
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146 <param name="fastq" ftype="fastq.gz" value="rif_resistant.fastq.gz" />
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147 <param name="output_format" value="txt" />
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148 <param name="platform" value="illumina" />
1
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149 <param name="options" value="no" />
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150 <output name="output_txt">
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151 <assert_contents>
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152 <has_line line="Drug-resistance: Drug-resistant" />
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153 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
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154 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
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155 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
1
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156 </assert_contents>
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157 </output>
0
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158 </test>
1
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159 <test>
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160 <param name="input_select" value="bam"/>
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161 <param name="bam_input" ftype="bam" value="rif_resistant.bam" />
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162 <param name="output_format" value="txt" />
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163 <param name="platform" value="illumina" />
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164 <param name="options" value="no" />
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165 <output name="output_txt">
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166 <assert_contents>
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167 <has_line line="Drug-resistance: Drug-resistant" />
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168 <has_line line="lineage2.2.2&#009;1.000&#009;East-Asian (Beijing)&#009;Beijing-RD105/RD207&#009;RD105;RD207" />
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169 <has_line line="Rifampicin&#009;R&#009;rpoB p.Asp435Val (1.00)" />
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170 <has_line line="763031&#009;Rv0667&#009;rpoB&#009;c.3225T>C&#009;1.000" />
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171 </assert_contents>
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172 </output>
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173 </test>
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174 </tests>
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175 <help><![CDATA[
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176 Summary
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177 =======
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178
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c2656b729ee9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tb-profiler commit a51548708ea975c0a7b135a2cbaa5d094f3c5602"
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179 The pipeline aligns reads to the H37Rv reference using bowtie2, BWA or minimap2 and then calls variants using GATK. These variants are then compared to a drug-resistance database. We also predict the number of reads supporting drug resistance variants as an insight into hetero-resistance (not applicable for minION data).
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180
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181 Produces a JSON output file by default.
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182
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183 ]]> </help>
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184 <citations>
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185 <citation type="bibtex">
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186 @UNPUBLISHED{Phelan2016,
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187 author = {Phelan, Jody},
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188 title = {TBProfiler},
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189 year = {2016},
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190 url = {https://github.com/jodyphelan/TBProfiler},
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191 }
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192 </citation>
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193 </citations>
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194 </tool>