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1 <tool id="my_VDM_tool" name="VDM_tool" version="1.0.0">
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2 <!--A simple description of the tool that will appear in the tool panel in Galaxy.-->
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3 <description>Map a mutation using in silico bulk segregant linkage analysis of pooled recombinant lines generated through backcrossing.</description>
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4 <!-- Handles exit codes in Galaxy. -->
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5 <stdio>
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6 <exit_code range="1:"/>
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7 </stdio>
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8 <requirements>
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9 <requirement type="package" version="3.2.1">R</requirement>
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10 <requirement type="package" version="1.2.0">getopt</requirement>
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11 </requirements>
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12
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13 <command>
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14 Rscript /home/fxue/galaxy/tools/my_VDM_tool/my_VDM_tool.R
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15 --inf "$inf"
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16 #if $species.species_select=="Celegans"
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17 --itype "$species.ce"
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18 #else if $species.species_select=="Zebrafish"
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19 --itype "$species.ze"
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20 #else if $species.species_select=="Brachypodium"
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21 --itype "$species.br"
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22 #else if $species.species_select=="Arabidopsis"
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23 --itype "$species.ar"
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24 #else if $species.species_select=="other"
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25 --itype "$species.ot"
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26 #end if
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27
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28 --qual $qual
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29 --thrup $thrup
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30 --thrlow $thrlow
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31
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32 #if $allfreq.allfreq_select=="AB"
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33 --allr "$allfreq.ab"
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34 #else if $allfreq.allfreq_select=="ratio"
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35 --allr "$allfreq.ratio"
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36 #end if
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37
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38 #if $only_snp.only_snp_select=="TRUE"
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39 --snp "$only_snp.true"
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40 #else if $only_snp.only_snp_select=="FALSE"
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41 --snp "$only_snp.false"
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42 #end if
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43
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44 --lsp $lsp
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45 --pcol "$pcol"
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46 --lcol "$lcol"
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47
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48 #if $xaxis.xaxis_select=="TRUE"
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49 --xstand $xaxis.true
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50 #else if $xaxis.xaxis_select=="FALSE"
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51 --xstand $xaxis.false
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52 #end if
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53
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54 --bsize $bsize
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55
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56 #if $binnorm.binnorm_select=="TRUE"
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57 --bnorm $binnorm.true
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58 #else if $binnorm.binnorm_select=="FALSE"
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59 --bnorm $binnorm.false
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60 #end if
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61
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62 #if $exclfiles.exclfiles_select=="FALSE"
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63 --exclf $exclfiles.false
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64 #else if $exclfiles.exclfiles_select=="TRUE"
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65 --exclf $exclfiles.true
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66 #end if
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67
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68
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69 --exclthr $exclthr
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70 --exclcol "$exclcol"
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71
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72 --parn "$parn"
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73 --outn "$outn"
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74 --pdfn "$pdfn"
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75
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76 </command>
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77 <inputs>
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78 <param type="data" name="inf" format="vcf" label="fastq file"/>
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79
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80 <conditional name="species">
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81 <param name="species_select" type="select" label="Select the species">
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82 <option value="Celegans">C. elegans</option>
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83 <option value="Zebrafish">Zebrafish</option>
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84 <option value="Brachypodium">Brachypodium</option>
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85 <option value="Arabidopsis">Arabidopsis</option>
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86 <option value="other">other</option>
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87 </param>
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88 <when value="Celegans">
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89 <param name="ce" type="hidden" value="C.elegans" label="The C. elegans chromosome numbers and lengths (in Mb)" help="C.elegans help"/>
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90 </when>
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91 <when value="Zebrafish">
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92 <param name="ze" type="hidden" value="Zebrafish" label="The Zebrafish chromosome numbers and lengths (in Mb)" help="Zebrafish help"/>
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93 </when>
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94 <when value="Brachypodium">
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95 <param name="br" type="hidden" value="Brachypodium" label="The Brachypodium chromosome numbers and lengths (in Mb)" help="Brachypodium help"/>
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96 </when>
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97 <when value="Arabidopsis">
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98 <param name="ar" type="hidden" value="Arabidopsis" label="The Arabidopsis chromosome numbers and lengths (in Mb)" help="Arabidopsis help"/>
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99 </when>
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100 <when value="other">
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101 <param name="ot" type="data" format="tabular" label="Select file with chromosome numbers and lengths (in Mb) from your history" help="Table consisting of chromosome number in column 1 and length (in Mb) in column 2 (e.g. 'CHRI 16' or 'CHR1 16') with no column header names, tab-delimitation, and no quotation marks in a .txt file"/>
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102 </when>
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103 </conditional>
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104
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105 <param type="float" name="qual" value="200" label="Filter by quality" help="Filter results based on quality value"/>
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106 <param type="float" name="thrup" value="1" label="upper threshold for homozygosity" help="Allele frequency values greater than or equal to this will be considered as homozygous ALT for barplots of frequency homozygous variants along chromosomes"/>
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107 <param type="float" name="thrlow" value="0" label="lower threshold for homozygosity" help="Allele frequency values less than or equal to this will be considered as homozygous for barplots of frequency homozygous REF variants along chromosomes"/>
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108
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109
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110 <conditional name="allfreq">
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111 <param name="allfreq_select" type="select" label="Select the source for allele frequency">
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112 <option value="AB">AB</option>
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113 <option value="ratio">AO/(AO+RO)</option>
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114 </param>
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115 <when value="AB">
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116 <param name="ab" type="hidden" value="AB" label="Use AB field (from Freebayes) as the value for allele frequency" help=" "/>
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117 </when>
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118 <when value="ratio">
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119 <param name="ratio" type="hidden" value="ratio" label="Use AO/(AO+RO) calculation (from Freebayes) as the value for allele frequency" help=" "/>
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120 </when>
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121 </conditional>
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122
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123 <conditional name="only_snp">
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124 <param name="only_snp_select" type="select" label="Select type of variants to use for plotting">
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125 <option value="TRUE">SNPs</option>
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126 <option value="FALSE">all</option>
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127 </param>
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128 <when value="TRUE">
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129 <param name="true" type="hidden" value="TRUE" label="Use only SNP variants" help=" "/>
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130 </when>
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131 <when value="FALSE">
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132 <param name="false" type="hidden" value="FALSE" label="Use all types of variants" help=" "/>
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133 </when>
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134 </conditional>
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135
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136 <param type="float" name="lsp" value="0.4" label="Loess span" help="Parameter that controls the smoothing of the Loess curve"/>
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137 <param type="text" name="pcol" value="black" label="Colour of scatterplot points" help="See below for list of supported colors"/>
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138 <param type="text" name="lcol" value="red" label="Colour of Loess curve" help="See below for list of supported colors"/>
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139
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140
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141 <conditional name="xaxis">
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142 <param name="xaxis_select" type="select" label="Spacing of the x-axis in plots">
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143 <option value="TRUE">True</option>
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144 <option value="FALSE">False</option>
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145 </param>
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146 <when value="TRUE">
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147 <param name="true" type="hidden" value="TRUE" label="Uniform spacing of the x-axis based on Mb" help="Scale of x-axis (in Mb) is fixed for the scatter plots and frequency plots across all chromosomes"/>
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148 </when>
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149 <when value="FALSE">
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150 <param name="false" type="hidden" value="FALSE" label="Variable spacing of the x-axis based on chromosome lengths" help="Scale of x-axis (in Mb) is dependent on chromosome length for the scatter plots and frequency plots for all chromosomes"/>
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151 </when>
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152 </conditional>
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153
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154 <param type="integer" name="bsize" value="1000000" label="bin size" help="Size of the bins (in bp) for barplot of frequency of homozygous variants along chromosomes"/>
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155
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156 <conditional name="binnorm">
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157 <param name="binnorm_select" type="select" label="Normalisation of y-axis in frequency barplots">
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158 <option value="TRUE">True</option>
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159 <option value="FALSE">False</option>
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160 </param>
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161 <when value="TRUE">
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162 <param name="true" type="hidden" value="TRUE" label="Normalised y-axis frequency values based on formula" help="Normalisation formula as in cloudmap paper"/>
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163 </when>
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164 <when value="FALSE">
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165 <param name="false" type="hidden" value="FALSE" label="Original frequency y-axis values" help=" "/>
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166 </when>
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167 </conditional>
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168
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169 <conditional name="exclfiles">
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170 <param name="exclfiles_select" type="select" label="Additional exclusion of variants by subtraction">
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171 <option value="FALSE">No</option>
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172 <option value="TRUE">Yes</option>
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173 </param>
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174 <when value="FALSE">
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175 <param name="false" type="hidden" value="FALSE" label="No additional variant subtraction" help=""/>
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176 </when>
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177 <when value="TRUE">
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178 <param name="true" type="data" format="tabular" label="Select variant lists to subtract from your history" help="Requires CHR POS DEPTH REF ALT columns- recommend directly using the output table generated by this tool or refer to it for desired format"/>
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179
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180 <param type="float" name="exclthr" value="0" label="Filter based on allelic ratio values" help="For filtering variant subtraction lists, only variants above this threshold value will be used for subtraction (e.g. 0 means all variants and 1 means only homozygous variants"/>
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181 <param type="text" name="exclcol" value="green" label="Colour of original loess curve (before additional variant subtraction)" help="See below for list of supported colors"/>
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182 </when>
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183 </conditional>
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184
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185 </inputs>
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186
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187 <outputs>
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188 <data name="parn" format="txt"/>
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189 <data name="outn" format="txt"/>
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190 <data name="pdfn" format="pdf"/>
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191 </outputs>
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192
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193 <tests>
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194 </tests>
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195
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196 <help>
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197 </help>
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198 </tool> |