annotate neat_genreads.xml @ 4:110fc7a9a016 draft

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author thondeboer
date Tue, 15 May 2018 16:45:22 -0400
parents edca797fa2b2
children 5bcfac4f8116
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1 <tool id="neat_genreads"
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2 name="NEAT-genReads"
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3 version="1.0.0"
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4 profile="16.04">
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5 <description>is a fine-grained read simulator</description>
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6 <requirements>
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7 <requirement type="package">numpy</requirement>
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8 <requirement type="package">scipy</requirement>
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9 </requirements>
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10 <command detect_errors="exit_code">
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11 <![CDATA[
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12 python2 $__tool_directory__/genReads.py
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13 #if $in_type.input_type == "built-in":
1
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14 -r ${in_type.reference.fields.path}
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15 #else:
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16 -r ${in_type.reference}
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17 #end if
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18 -R $read_length
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19 -c $coverage
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20 #if $stats.error_model_cond.error_model == 'average_rate' and $stats.error_model_cond.error_rate != '':
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21 -E $stats.error_model_cond.error_rate
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22 #elif $stats.error_model_cond.error_model == 'error_model_file':
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23 -e $stats.error_model_cond.error_file
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24 #end if
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25 #if $stats.mut_rate_cond.mut_rate == 'average_rate' and $stats.mut_rate_cond.error_rate != '':
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26 -M $stats.mut_rate_cond.error_rate
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27 #elif $stats.mut_rate_cond.mut_rate == 'error_model_file':
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28 -m stats.mut_rate_cond.error_file
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29 #elif $stats.mut_rate_cond.mut_rate == 'error_model_bed':
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30 -Mb stats.mut_rate_cond.error_file_bed
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31 #end if
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32 #if $stats.gc_file:
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33 --gc-model $stats.gc_file
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34 #end if
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35 #if $stats.ploidy != 2 and $stats.ploidy > 0:
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36 -p $stats.ploidy
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37 #end if
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38 -o $out_options.prefix
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39 #if $lib_type_cond.lib_type == "paired":
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40 #if $lib_type_cond.insert_mod_cond.insert_mod == 'fixed_insert':
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41 --pe $lib_type_cond.insert_mod_cond.frag_length $lib_type_cond.insert_mod_cond.frag_length_sd
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42 #else:
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43 --pe-model $lib_type_cond.insert_mod_cond.insert_file
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44 #end if
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45 #end if
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46 $out_options.golden_bam
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47 $out_options.golden_vcf
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48 #if $target_vcf_cond.target_vcf == "use_vcf":
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49 -v ${target_vcf_cond.target_file}
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50 #end if
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51 #if $target_cond.target == "targeted":
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52 -t ${target_cond.target_file}
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53 -to ${target_cond.off_target}
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54 #end if
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55 #if $stats.seed != "":
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56 --rng $stats.seed
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57 #end if
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58 $out_options.compress
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59 $out_options.bypass
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60 #if $out_options.compress:
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61 #if not $out_options.bypass:
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62 && mv "${out_options.prefix}_read1.fq.gz" read1.fq.gz
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63 #if $lib_type_cond.lib_type == "paired":
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64 && mv "${out_options.prefix}_read2.fq.gz" read2.fq.gz
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65 #end if
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66 #end if
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67 #if $out_options.golden_bam != "":
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68 && mv "${out_options.prefix}_golden.bam" golden.bam
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69 #end if
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70 #if $out_options.golden_vcf != "":
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71 && gunzip "${out_options.prefix}_golden.vcf.gz" && mv "${out_options.prefix}_golden.vcf" golden.vcf
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72 #end if
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73 #else:
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74 #if not $out_options.bypass:
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75 && mv "${out_options.prefix}_read1.fq" read1.fq
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76 #if $lib_type_cond.lib_type == "paired":
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77 && mv "${out_options.prefix}_read2.fq" read2.fq
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78 #end if
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79 #end if
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80 #if $out_options.golden_bam != "":
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81 && mv "${out_options.prefix}_golden.bam" golden.bam
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82 #end if
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83 #if $out_options.golden_vcf != "":
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84 && mv "${out_options.prefix}_golden.vcf" golden.vcf
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85 #end if
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86 #end if
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87 ]]>
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88 </command>
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89 <inputs>
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90
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91 <conditional name="in_type">
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92 <param name="input_type" type="select" label="Use a built-in FASTA file or one from the history?">
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93 <option value="built-in">Built-in</option>
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94 <option value="history">History file</option>
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95 </param>
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96 <when value="built-in">
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97 <param name="reference"
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98 type="select"
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99 label="Select a built-in reference sequence"
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100 help="The reference sequence that will be used as the basis for the simulated reads">
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101 <options from_data_table="all_fasta" />
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102 </param>
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103 </when>
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104 <when value="history">
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105 <param name="reference"
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106 type="data"
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107 format="fasta"
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108 label="The reference sequence (FASTA format)"
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109 help="The reference sequence that will be used as the basis for the simulated reads"
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110 />
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111 </when>
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112 </conditional>
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113
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114 <param name="read_length"
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115 type="integer"
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116 value="101"
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117 size="4"
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118 min="30"
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119 label="Read length"
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120 help="The read length for the simulated reads [-R]"
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121 />
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122 <param name="coverage"
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123 type="integer"
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124 value="10"
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125 size="4"
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126 min="1"
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127 label="Coverage"
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128 help="Average coverage across entire dataset [-c]"
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129 />
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130
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131 <conditional name="lib_type_cond">
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132 <param name="lib_type"
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133 type="select"
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134 label="Single-end or paired-end sequencing library?"
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135 >
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136 <option value="paired">Paired-end</option>
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137 <option value="single">Single-end</option>
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138 </param>
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139 <when value="paired">
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140 <conditional name="insert_mod_cond">
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141 <param name="insert_mod"
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142 type="select"
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143 label="Used fixed insert size or empirical model?"
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144 >
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145 <option value="fixed_insert">Fixed insert size</option>
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146 <option value="model_insert">Use model file</option>
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147 </param>
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148 <when value="fixed_insert">
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149 <param name="frag_length"
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150 type="integer"
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151 value="300"
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152 size="5"
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153 min="50"
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154 label="Fragment length"
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155 help="The average total size of the fragment"
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156 />
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157 <param name="frag_length_sd"
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158 type="integer"
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159 value="30"
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160 size="4"
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161 min="0"
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162 label="Fragment length SD"
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163 help="The standard deviation for the average total size of the fragment"
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164 />
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165 </when>
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166 <when value="model_insert">
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167 <param name="insert_file"
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168 optional="false"
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169 type="data"
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170 format="txt"
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171 label="Emperical insert size model file"
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172 help="Insert size model file, created by computeFraglen (python pickle format) [-pe-model]"
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173 />
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174 </when>
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175 </conditional>
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176 </when>
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177 </conditional>
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178
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179 <conditional name="target_cond">
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180 <param name="target"
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181 type="select"
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182 label="Limit the simulated reads to target area?"
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183 >
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184 <option value="full">No - Use complete reference</option>
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185 <option value="targeted">Yes - Limit to target region</option>
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186 </param>
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187 <when value="targeted">
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188 <param name="target_file"
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189 type="data"
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190 format="bed"
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191 label="Target region file"
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192 help="The simulated reads will primarily orginate from the target region [-t]"
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193 />
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194 <param name="off_target"
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195 type="float"
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196 value="0.02"
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197 min="0"
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198 max="1"
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199 label="Off-target converage"
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200 help="The coverage outside the target region will be this fraction. 1-this will be on-target coverage [-to]"
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201 />
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202 </when>
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203 </conditional>
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204
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205 <conditional name="target_vcf_cond">
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206 <param name="target_vcf"
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207 type="select"
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208 label="Use a VCF file to seed the simulation?"
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209 >
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210 <option value="no_vcf">No</option>
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211 <option value="use_vcf">Yes</option>
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212 </param>
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213 <when value="use_vcf">
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214 <param name="target_file"
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215 type="data"
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216 format="vcf"
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217 label="Input VCF file"
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218 help="Variants from this VCF will be inserted into the simulated sequence with 100% certainty [-v]"
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219 />
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220 </when>
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221 </conditional>
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222
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223 <section name="stats"
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224 title="Miscellanous settings"
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225 expanded="false"
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226 help="The settings for the error rates etc. for the model"
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227 >
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228 <param name="ploidy"
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229 type="integer"
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230 value="2"
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231 min="1"
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232 max="10"
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233 optional="false"
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234 label="Ploidy of the genome"
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235 help=""
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236 />
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237 <conditional name="error_model_cond">
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238 <param name="error_model" type="select" label="Sequencing error rate model">
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239 <option value="average_rate">Set an average rate</option>
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240 <option value="error_model_file">Use an emperical model file</option>
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241 </param>
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242 <when value="average_rate">
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243 <param name="error_rate"
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244 optional="true"
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245 type="float"
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246 value=""
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247 min="0"
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248 max="0.3"
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249 label="Average sequencing error rate (0-0.3)"
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250 help="Leave blank to use default. The sequencing error rate model is rescaled to make this the average value [-E]"
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251 />
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252 </when>
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253 <when value="error_model_file">
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254 <param name="error_file"
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255 optional="false"
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256 type="data"
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257 format="txt"
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258 label="Emperical error rate model file"
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259 help="Error rate model file, created by genSeqErrorModel.py (python pickle format) [-e]"
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260 />
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261 </when>
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262 </conditional>
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263
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264 <conditional name="mut_rate_cond">
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265 <param name="mut_rate" type="select" label="Mutation rate model">
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266 <option value="average_rate">Set an average mutation rate</option>
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267 <option value="error_model_file">Use a PICKLE file with mutation rates</option>
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268 <option value="error_model_bed">Use a BED file with mutation rates</option>
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269 </param>
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270 <when value="average_rate">
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271 <param name="error_rate"
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272 optional="true"
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273 type="float"
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274 value=""
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275 min="0"
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276 max="0.3"
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277 label="Average mutation rate (0-0.3)"
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278 help="Leave blank to use default. The mutation rate model is rescaled to make this the average value. These random mutations are inserted in addition to the once specified in the -v option [-M]"
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279 />
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280 </when>
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281 <when value="error_model_file">
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282 <param name="error_file"
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283 optional="true"
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284 type="data"
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285 format="txt"
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286 label="Mutation rate model file"
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287 help="Mutation rate model file, created by genMutModel (python pickle format) [-m]"
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288 />
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289 </when>
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290 <when value="error_model_bed">
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291 <param name="error_file_bed"
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292 optional="true"
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293 type="data"
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294 format="bed"
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295 label="Mutation rate model BED file"
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296 help="Error rate model file, in BED format [-Mb]"
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297 />
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298 </when>
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299 </conditional>
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300
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301 <param name="gc_file"
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302 optional="true"
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303 type="data"
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304 format="txt"
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305 label="Emperical GC-bias model file"
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306 help="Empirical GC coverage bias distribution. Can be generated using computeGC (python pickle format) [--gc-model]"
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307 />
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308 <param name="seed"
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309 type="integer"
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310 min="1"
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311 optional="true"
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312 label="Random seed"
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313 help="Identical seed values should produce indentical runs, so things like read locations, variant positions, error positions etc. should all be the same [--rng]"
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314 />
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315
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316 </section>
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317
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318 <section name="out_options"
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319 title="Optional output options"
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320 expanded="false"
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321 help="Optional output options"
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322 >
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323
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324 <param name="prefix"
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325 type="text"
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326 label="Output prefix"
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327 value="simulated_reads"
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328 size="40"
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329 help="Prefix for the name of the output simulated reads and other files [-o]"
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330 />
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331
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332 <param name="golden_vcf"
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333 type="boolean"
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334 checked="true"
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335 truevalue="--vcf"
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336 falsevalue=""
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337 label="Create the golden VCF file?"
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338 help="The golden VCF file will contain the golden truth for all variants created [--vcf]"
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339 />
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340 <param name="golden_bam"
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341 type="boolean"
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342 checked="true"
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343 truevalue="--bam"
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344 falsevalue=""
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345 label="Create the golden BAM file?"
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346 help="The golden BAM file will contain the golden truth for all variants created [--bam]"
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347 />
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348 <param name="compress"
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349 type="boolean"
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350 checked="true"
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351 truevalue="--gz"
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352 falsevalue=""
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353 label="Compress the FASTQ and VCF files with gzip? [--gz]"
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354 help=""
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355 />
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356 <param name="bypass"
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357 type="boolean"
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358 checked="false"
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359 truevalue="--no-fastq"
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360 falsevalue=""
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361 label="Bypass generation of FASTQ files?"
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362 help="If checked, FASTQ files will not be created. Only BAM and VCF files will (if selected) [--no-fastq]"
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363 />
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364 </section>
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365 </inputs>
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366 <outputs>
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367 <data format="fastqsanger"
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368 name="out_file1"
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369 from_work_dir="read1.fq"
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370 label="${out_options.prefix}_read1.fq"
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371 metadata_source="in_type.reference">
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372 <filter>not out_options['compress'] and not out_options['bypass']</filter>
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373 </data>
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374 <data format="fastqsanger"
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375 name="out_file2"
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376 from_work_dir="read2.fq"
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377 label="${out_options.prefix}_read2.fq"
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378 metadata_source="in_type.reference">
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379 <filter>not out_options['compress'] and not out_options['bypass'] and lib_type_cond['lib_type'] == 'paired'</filter>
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380 </data>
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381 <data format="bam"
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382 name="out_bam"
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383 from_work_dir="golden.bam"
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384 label="${out_options.prefix}_golden.bam"
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385 metadata_source="in_type.reference">
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386 <filter>out_options['golden_bam']</filter>
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387 </data>
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388 <data format="vcf"
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389 name="out_vcf"
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390 from_work_dir="golden.vcf"
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391 label="${out_options.prefix}_golden.vcf"
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392 metadata_source="in_type.reference">
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393 <filter>out_options['golden_vcf']</filter>
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394 </data>
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395 <data format="fastqsanger.gz"
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396 name="out_file1gz"
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397 from_work_dir="read1.fq.gz"
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398 label="${out_options.prefix}_read1.fq.gz"
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399 metadata_source="in_type.reference">
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400 <filter>not out_options['bypass'] and out_options['compress']</filter>
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401 </data>
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402 <data format="fastqsanger.gz"
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403 name="out_file2gz"
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404 from_work_dir="read2.fq.gz"
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405 label="${out_options.prefix}_read2.fq.gz"
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406 metadata_source="in_type.reference">
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407 <filter>not out_options['bypass'] and lib_type_cond['lib_type'] == 'paired' and out_options['compress']</filter>
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408 </data>
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409 </outputs>
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thondeboer
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410 <tests>
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411
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412 <test>
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413 <conditional name="in_type">
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414 <param name="input_type" value="history"/>
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415 <param name="reference" value="chrMT.fa" format="fasta"/>
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416 </conditional>
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417 <conditional name="lib_type_cond">
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418 <param name="lib_type" value="single"/>
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419 </conditional>
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420 <section name="stats">
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421 <param name="seed" value="1"/>
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422 </section>
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423 <param name="read_length" value="101"/>
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424 <section name="out_options">
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425 <param name="prefix" value="out"/>
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426 <param name="golden_bam" value="false"/>
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427 <param name="golden_vcf" value="false"/>
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428 <param name="compress" value="false"/>
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429 </section>
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430 <output name="out_file1" file="chrMT_read1.fq" compare="diff"/>
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431 </test>
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432
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433 <test>
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434 <conditional name="in_type">
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435 <param name="input_type" value="history"/>
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436 <param name="reference" value="chrMT.fa" format="fasta"/>
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437 </conditional>
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438 <conditional name="lib_type_cond">
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439 <param name="lib_type" value="paired"/>
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440 <conditional name="insert_mod_cond">
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441 <param name="insert_mod" value="fixed_insert"/>
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442 <param name="frag_length" value="300"/>
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443 <param name="frag_length_sd" value="30"/>
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444 </conditional>
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445 </conditional>
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446 <section name="stats">
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447 <param name="seed" value="1"/>
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448 </section>
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449 <param name="read_length" value="101"/>
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450 <section name="out_options">
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451 <param name="prefix" value="out"/>
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452 <param name="golden_bam" value="false"/>
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453 <param name="golden_vcf" value="false"/>
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454 <param name="compress" value="false"/>
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455 </section>
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456 <output name="out_file1" file="chrMT-PE_read1.fq" compare="diff"/>
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457 <output name="out_file2" file="chrMT-PE_read2.fq" compare="diff"/>
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458 </test>
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459
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460 <test>
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461 <conditional name="in_type">
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462 <param name="input_type" value="history"/>
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463 <param name="reference" value="chrMT.fa" format="fasta"/>
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464 </conditional>
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465 <conditional name="lib_type_cond">
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466 <param name="lib_type" value="paired"/>
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467 <conditional name="insert_mod_cond">
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468 <param name="insert_mod" value="fixed_insert"/>
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469 <param name="frag_length" value="300"/>
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470 <param name="frag_length_sd" value="30"/>
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471 </conditional>
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472 </conditional>
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473 <section name="stats">
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474 <param name="seed" value="1"/>
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475 </section>
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476 <param name="read_length" value="101"/>
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477 <section name="out_options">
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478 <param name="prefix" value="out"/>
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479 <param name="golden_bam" value="true"/>
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480 <param name="golden_vcf" value="true"/>
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481 <param name="compress" value="false"/>
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482 </section>
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483 <output name="out_file1" file="chrMT-PE-VCF-BAM_read1.fq" compare="diff"/>
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484 <output name="out_file2" file="chrMT-PE-VCF-BAM_read2.fq" compare="diff"/>
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485 <output name="out_bam" file="chrMT-PE-VCF-BAM.bam" compare="diff"/>
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486 <output name="out_vcf" file="chrMT-PE-VCF-BAM.vcf" compare="diff" lines_diff="2"/>
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487 <assert_stdout has_text="Writing output VCF..."/>
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488 </test>
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489
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diff changeset
490 <test>
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diff changeset
491 <conditional name="in_type">
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492 <param name="input_type" value="history"/>
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493 <param name="reference" value="chrMT.fa" format="fasta"/>
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494 </conditional>
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495 <conditional name="lib_type_cond">
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496 <param name="lib_type" value="paired"/>
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497 <conditional name="insert_mod_cond">
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498 <param name="insert_mod" value="fixed_insert"/>
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499 <param name="frag_length" value="300"/>
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500 <param name="frag_length_sd" value="30"/>
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501 </conditional>
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502 </conditional>
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503 <section name="stats">
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504 <param name="seed" value="1"/>
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505 </section>
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506 <param name="read_length" value="101"/>
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507 <section name="out_options">
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508 <param name="prefix" value="out"/>
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509 <param name="golden_bam" value="true"/>
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510 <param name="golden_vcf" value="true"/>
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511 <param name="compress" value="false"/>
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512 </section>
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513 <conditional name="target_vcf_cond">
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514 <param name="target_vcf" value="use_vcf"/>
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515 <param name="target_file" value="chrMT-PE-VCF-BAM.vcf"/>
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516 </conditional>
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517 <output name="out_file1" file="chrMT-PE-VCF-BAM-vcf_read1.fq" compare="diff"/>
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518 <output name="out_file2" file="chrMT-PE-VCF-BAM-vcf_read2.fq" compare="diff"/>
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519 <output name="out_bam" file="chrMT-PE-VCF-BAM-vcf.bam" compare="diff"/>
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520 <output name="out_vcf" file="chrMT-PE-VCF-BAM-vcf.vcf" compare="diff" lines_diff="2"/>
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521 <assert_stdout has_text="Writing output VCF..."/>
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522 </test>
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523
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diff changeset
524 <test>
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diff changeset
525 <conditional name="in_type">
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526 <param name="input_type" value="history"/>
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527 <param name="reference" value="chrMT.fa" format="fasta"/>
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528 </conditional>
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parents:
diff changeset
529 <conditional name="lib_type_cond">
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530 <param name="lib_type" value="paired"/>
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531 <conditional name="insert_mod_cond">
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532 <param name="insert_mod" value="fixed_insert"/>
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533 <param name="frag_length" value="300"/>
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534 <param name="frag_length_sd" value="30"/>
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535 </conditional>
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536 </conditional>
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diff changeset
537 <section name="stats">
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538 <param name="seed" value="1"/>
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diff changeset
539 </section>
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540 <param name="read_length" value="101"/>
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thondeboer
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541 <section name="out_options">
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542 <param name="prefix" value="out"/>
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543 <param name="golden_bam" value="true"/>
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thondeboer
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544 <param name="golden_vcf" value="true"/>
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545 <param name="compress" value="false"/>
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diff changeset
546 </section>
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diff changeset
547 <conditional name="target_cond">
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548 <param name="target" value="targeted"/>
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parents:
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549 <param name="target_file" value="chrMT-Targets.bed"/>
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thondeboer
parents:
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550 <param name="off_target" value="0.02"/>
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551 </conditional>
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diff changeset
552 <output name="out_file1" file="chrMT-PE-VCF-BAM-Targeted_read1.fq" compare="diff"/>
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553 <output name="out_file2" file="chrMT-PE-VCF-BAM-Targeted_read2.fq" compare="diff"/>
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diff changeset
554 <output name="out_bam" file="chrMT-PE-VCF-BAM-Targeted.bam" compare="diff"/>
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parents:
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555 <output name="out_vcf" file="chrMT-PE-VCF-BAM-Targeted.vcf" compare="diff" lines_diff="2"/>
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diff changeset
556 <assert_stdout has_text="Writing output VCF..."/>
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diff changeset
557 </test>
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558
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diff changeset
559 <test>
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diff changeset
560 <conditional name="in_type">
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561 <param name="input_type" value="history"/>
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562 <param name="reference" value="chrMT.fa" format="fasta"/>
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diff changeset
563 </conditional>
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diff changeset
564 <conditional name="lib_type_cond">
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565 <param name="lib_type" value="paired"/>
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parents:
diff changeset
566 <conditional name="insert_mod_cond">
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567 <param name="insert_mod" value="fixed_insert"/>
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568 <param name="frag_length" value="300"/>
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parents:
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569 <param name="frag_length_sd" value="30"/>
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570 </conditional>
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571 </conditional>
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diff changeset
572 <section name="stats">
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573 <param name="seed" value="1"/>
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diff changeset
574 </section>
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575 <param name="read_length" value="101"/>
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parents:
diff changeset
576 <section name="out_options">
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577 <param name="prefix" value="out"/>
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parents:
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578 <param name="golden_bam" value="true"/>
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579 <param name="golden_vcf" value="true"/>
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580 <param name="compress" value="true"/>
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parents:
diff changeset
581 </section>
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thondeboer
parents:
diff changeset
582 <!-- The decompress does not seem to work
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583 <output name="out_file1" file="chrMT-PE-VCF-BAM-gz_read1.fq.gz" compare="diff" decompress="true"/>
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584 <output name="out_file2" file="chrMT-PE-VCF-BAM-gz_read2.fq.gz" compare="diff" decompress="true"/>
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thondeboer
parents:
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585 -->
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586 <output name="out_bam" file="chrMT-PE-VCF-BAM-gz.bam" compare="diff"/>
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587 <output name="out_vcf" file="chrMT-PE-VCF-BAM-gz.vcf" compare="diff" lines_diff="2"/>
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588 <assert_stdout has_text="Writing output VCF..."/>
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589 </test>
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590
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591 <test>
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592 <conditional name="in_type">
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593 <param name="input_type" value="history"/>
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594 <param name="reference" value="chrMT.fa" format="fasta"/>
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595 </conditional>
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596 <conditional name="lib_type_cond">
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597 <param name="lib_type" value="paired"/>
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598 <conditional name="insert_mod_cond">
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599 <param name="insert_mod" value="fixed_insert"/>
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600 <param name="frag_length" value="500"/>
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601 <param name="frag_length_sd" value="50"/>
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602 </conditional>
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603 </conditional>
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604 <conditional name="error_model_cond">
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605 <param name="error_model" value="average_rate"/>
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606 <param name="error_rate" value="0.123"/>
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607 </conditional>
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608 <conditional name="mut_rate_cond">
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609 <param name="mut_rate" value="average_rate"/>
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610 <param name="error_rate" value="0.123"/>
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611 </conditional>
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612 <section name="stats">
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613 <param name="seed" value="123"/>
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614 <param name="ploidy" value="3"/>
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615 </section>
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616 <param name="read_length" value="151"/>
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617 <param name="coverage" value="20"/>
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618 <section name="out_options">
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619 <param name="prefix" value="out"/>
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620 <param name="golden_bam" value="true"/>
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621 <param name="golden_vcf" value="true"/>
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622 <param name="compress" value="false"/>
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623 </section>
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624 <output name="out_file1" file="chrMT-PE-VCF-BAM-panic_read1.fq" compare="diff"/>
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625 <output name="out_file2" file="chrMT-PE-VCF-BAM-panic_read2.fq" compare="diff"/>
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626 <output name="out_bam" file="chrMT-PE-VCF-BAM-panic.bam" compare="diff"/>
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627 <output name="out_vcf" file="chrMT-PE-VCF-BAM-panic.vcf" compare="diff" lines_diff="2"/>
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628 <assert_stdout has_text="Writing output VCF..."/>
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629 </test>
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630
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631
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632 </tests>
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633 </tool>