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"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/optitype commit 703114ab7ad18b1b0e824b103f1df213448c6e97-dirty"
author jjohnson
date Tue, 09 Feb 2021 15:41:49 +0000
parents 54c9c71dabe8
children
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1 <tool id="optitype" name="OptiType" version="1.3.5">
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2 <description>HLA genotyping predictions from NGS data</description>
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3 <requirements>
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4 <requirement type="package" version="1.3.5">optitype</requirement>
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5 </requirements>
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6 <command detect_errors="aggressive">
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7 <![CDATA[
3902a76bf089 "planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/optitype commit 92a9a2f36072d19783d111ae15843c47a7a85c87"
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8 #set $fastqs = []
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9 #if str( $fastq_input.fastq_input_selector ) == "paired":
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10 ln -s '${fastq_input.fastq_input1}' reads_1.fastq
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11 && ln -s '${fastq_input.fastq_input2}' reads_2.fastq
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12 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
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13 #elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
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14 ln -s '${fastq_input.fastq_input1.forward}' reads_1.fastq
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15 && ln -s '${fastq_input.fastq_input1.reverse}' reads_2.fastq
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16 #set $fastqs = ['reads_1.fastq','reads_2.fastq']
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17 #elif str( $fastq_input.fastq_input_selector ) == "single":
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18 ln -s '${fastq_input.fastq_input1}' reads.fastq
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19 #set $fastqs = ['reads.fastq']
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20 #end if
1
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21 && RAZERS3=`which razers3`
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22 && sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\${GALAXY_SLOTS}/" > config.ini
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23 #set $input_fq = ' '.join($fastqs)
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24 && OptiTypePipeline.py
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25 $read_type --input ${' '.join($fastqs)}
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26 #if str($beta) != '':
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27 --beta $beta
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28 #end if
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29 #if str($enumerations) != '':
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30 --enumerate $enumerations
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31 #end if
1
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32 --config "`pwd`/config.ini"
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33 --outdir $outdir
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34 && cp $outdir/*/*_coverage_plot.pdf $coverage_plot
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35 && cp $outdir/*/*_result.tsv $result
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36 ]]>
1
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37 </command>
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38 <configfiles>
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39 <configfile name="optitype_config"><![CDATA[
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40 [mapping]
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41
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42 # Absolute path to RazerS3 binary, and number of threads to use for mapping
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43
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44 razers3=path_to_razers3
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45 threads=16
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46
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47 [ilp]
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48
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49 # A Pyomo-supported ILP solver. The solver must be globally accessible in the
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50 # environment OptiType is run, so make sure to include it in PATH.
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51 # Note: this is NOT a path to the solver binary, but a keyword argument for
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52 # Pyomo. Examples: glpk, cplex, cbc.
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53
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54 solver=$solver
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55 threads=1
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56
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57 [behavior]
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58
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59 # tempdir=/path/to/tempdir # we may enable this setting later. Not used now.
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60
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61 # Delete intermediate bam files produced by RazerS3 after OptiType finished
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62 # loading them. If you plan to re-analyze your samples with different settings
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63 # disabling this option can be a time-saver, as you'll be able to pass the bam
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64 # files to OptiType directly as input and spare the expensive read mapping
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65 # step.
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66
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67 deletebam=true
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68
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69 # In paired-end mode one might want to use reads with just one mapped end (e.g.,
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70 # the other end falls outside the reference region). This setting allows the
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71 # user to keep them with an optionally reduced weight. A value of 0 means they
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72 # are discarded for typing, 0.2 means single reads are "worth" 20% of paired
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73 # reads, and a value of 1 means they are treated as valuable as properly mapped
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74 # read pairs. Note: unpaired reads will be reported on the result coverage plots
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75 # for completeness, regardless of this setting.
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76
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77 unpaired_weight=$unpaired_weight
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78
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79 # We call a read pair discordant if its two ends best-map to two disjoint sets
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80 # of alleles. Such reads can be either omitted or either of their ends treated
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81 # as unpaired hits. Note: discordant read pairs are reported on the coverage
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82 # plots as unpaired reads, regardless of this setting.
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83
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84 use_discordant=$use_discordant
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85 ]]></configfile>
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86 </configfiles>
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87 <inputs>
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88 <conditional name="fastq_input">
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89 <param name="fastq_input_selector" type="select" label="Single or Paired-end reads" help="Select between paired and single end data">
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90 <option value="paired">Paired</option>
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91 <option value="single">Single</option>
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92 <option value="paired_collection">Paired Collection</option>
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93 </param>
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94 <when value="paired">
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95 <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
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96 <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
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97 </when>
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98 <when value="single">
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99 <param name="fastq_input1" type="data" format="fastqsanger" label="Select fastq dataset" help="Specify dataset with single reads"/>
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100 </when>
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101 <when value="paired_collection">
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102 <param name="fastq_input1" format="fastqsanger" type="data_collection" collection_type="paired" label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
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103 </when>
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104 </conditional>
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105 <param name="read_type" type="select" label="Nucleotide Type" help="">
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106 <option value="--rna">RNA</option>
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107 <option value="--dna">DNA</option>
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108 </param>
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109 <param name="beta" type="float" value="" min="0.0" max="0.1" optional="true" label="homozygosity beta" help="The beta value for for homozygosity detection (Leave blank for default: 0.009)"/>
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110 <param name="enumerations" type="integer" value="" min="1" max="5" optional="true" label="Enumerations" help="The number of enumerations (Leave blank for default: 1)"/>
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111 <param name="solver" type="select" label="ILP solver" help="">
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112 <option value="glpk">glpk</option>
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113 <!--
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114 <option value="cbc">cbc</option>
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115 -->
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116 </param>
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117 <param name="unpaired_weight" type="float" value="0" min="0.0" max="1.0" label="unpaired_weight">
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118 <help><![CDATA[
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119 In paired-end mode one might want to use reads with just one mapped end (e.g.,
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120 the other end falls outside the reference region). This setting allows the
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121 user to keep them with an optionally reduced weight. A value of 0 means they
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122 are discarded for typing, 0.2 means single reads are "worth" 20% of paired
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123 reads, and a value of 1 means they are treated as valuable as properly mapped
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124 read pairs. Note: unpaired reads will be reported on the result coverage plots
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125 for completeness, regardless of this setting. ]]>
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126 </help>
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127 </param>
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128 <param name="use_discordant" type="boolean" truevalue="true" falsevalue="false" checked="false" label="use_discordant">
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129 <help><![CDATA[
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130 We call a read pair discordant if its two ends best-map to two disjoint sets
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131 of alleles. Such reads can be either omitted or either of their ends treated
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132 as unpaired hits. Note: discordant read pairs are reported on the coverage
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133 plots as unpaired reads, regardless of this setting. ]]>
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134 </help>
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135 </param>
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136 <param name="outdir" type="hidden" value="output_dir"/>
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137 </inputs>
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138 <outputs>
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139 <data format="pdf" name="coverage_plot" label="${tool.name} on ${on_string} coverage_plot.pdf"/>
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140 <data format="tabular" name="result" label="${tool.name} on ${on_string} result.tsv"/>
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141 </outputs>
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142 <tests>
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143 <test>
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144 <conditional name="fastq_input">
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145 <param name="fastq_input_selector" value="paired"/>
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146 <param name="fastq_input1" ftype="fastqsanger" value="rna/CRC_81_N_1_fished.fastq"/>
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147 <param name="fastq_input2" ftype="fastqsanger" value="rna/CRC_81_N_2_fished.fastq"/>
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148 </conditional>
2
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149 <param name="read_type" value="--rna"/>
1
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150 <output name="result">
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151 <assert_contents>
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152 <has_text text="A*31:01" />
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153 </assert_contents>
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154 </output>
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155 </test>
2
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156 <test>
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157 <conditional name="fastq_input">
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158 <param name="fastq_input_selector" value="paired"/>
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159 <param name="fastq_input1" ftype="fastqsanger" value="exome/NA11995_SRR766010_1_fished.fastq"/>
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160 <param name="fastq_input2" ftype="fastqsanger" value="exome/NA11995_SRR766010_2_fished.fastq"/>
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161 </conditional>
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162 <param name="read_type" value="--dna"/>
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163 <param name="unpaired_weight" value="0.2"/>
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164 <output name="result">
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165 <assert_contents>
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166 <has_text text="A*01:01" />
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167 </assert_contents>
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168 </output>
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169 </test>
1
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170 </tests>
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171 <help>
0
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172 <![CDATA[
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173 **OptiType**
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174 ============
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175
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176 OptiType_ is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.
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177
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178 **INPUTS**
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179
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180 RNA or DNA sequences in fastq format.
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181
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182 **OPTIONS**
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183
1
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184 --beta <BETA_VALUE> The beta value for for homozygosity detection (see cited paper).
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185 Default: 0.009. Handle with care.
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186 --enumerate <ENUMERATIONS> Number of enumerations.
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187 OptiType will output the optimal solution and the top N-1 suboptimal solutions in the results.
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188 Default: 1
0
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189
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190
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191 **OUTPUTS**
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192
1
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193 result.tsv A TAB-separated file of HLA genotyping predictions:
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194
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195 ::
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196
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197 A1 A2 B1 B2 C1 C2 Reads Objective
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198 0 A*31:01 A*68:01 B*40:01 B*51:01 C*15:02 C*03:04 132 128.43599999999998
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199
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200
1
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201 coverage_plot.pdf Plots of coverage of HLA genotyping predictions
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202
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203 .. _OptiType: https://github.com/FRED-2/OptiType
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204 ]]>
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205 </help>
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206 <citations>
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207 <citation type="doi">10.1093/bioinformatics/btu548</citation>
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208 </citations>
0
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209 </tool>