annotate macros.xml @ 1:fcf1bc63ed06 draft default tip

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author dave
date Thu, 26 Sep 2019 09:28:27 -0400
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1 <?xml version="1.0"?>
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2 <macros>
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3 <token name="@VERSION@">4.0.5.1</token>
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4 <token name="@WRAPPER_VERSION@">@VERSION@+galaxy</token>
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5
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6 <xml name="requirements">
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7 <requirements>
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8 <requirement type="package" version="@VERSION@">gatk4</requirement>
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9 <requirement type="package" version="0.2.5">tabix</requirement>
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10 <requirement type="package" version="1.9">samtools</requirement>
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11 <yield />
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12 </requirements>
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13 </xml>
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14
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15 <!--Hacky way to determine GATK version, for display in tool info-->
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16 <xml name="version_cmd">
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17 <version_command>gatk SortSam --version 2>&amp;1 | grep Version | cut -d ':' -f 2</version_command>
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18 </xml>
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19
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20 <!--Command token, java options should not be hard coded here.-->
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21 <token name="@CMD_BEGIN@">gatk --java-options "\$_JAVA_OPTIONS"</token>
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22
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23 <!--Define sections that parameters could exist within.-->
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24 <template name="set_sections">
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25 #set global $sections = ['', 'optional.', 'advanced.', 'common.', 'deprecated.']
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26 </template>
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27
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28 <!--Reference genome handling-->
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29 <!--One template each for the different reference genome parameter names.-->
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30 <!--TODO: Can the reference parameters all be the same?-->
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31 <xml name="ref_sel">
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32 <conditional name="reference_source">
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33 <param name="reference_source_selector" type="select" label="Choose the source for the reference list">
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34 <option value="cached">Locally cached</option>
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35 <option value="history">History</option>
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36 <option value="no_ref" selected="true">Do not pass</option>
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37 </param>
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38 <when value="cached">
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39 <param name="reference_sequence" type="select" label="Reference" help="Reference sequence file." >
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40 <options from_data_table="all_fasta" >
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41 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
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42 </options>
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43 </param>
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44 </when>
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45 <when value="history">
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46 <param name="reference_sequence" type="data" format="fasta" label="Reference" help="Reference sequence file." />
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47 </when>
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48 <when value="no_ref" />
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49 </conditional>
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50 </xml>
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51
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52 <template name="ref_opts">
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53 #for $sect in $sections
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54 #if $varExists($sect + "reference_source.reference_source_selector")
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55 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
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56 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
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57 --reference $getVar($sect + "reference_source.reference_sequence.fields.path")
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58 #else
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59 --reference reference.fa
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60 #end if
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61 #end if
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62 #end if
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63 #end for
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64 </template>
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65
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66 <template name="picard_ref_opts">
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67 #for $sect in $sections
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68 #if $varExists($sect + "reference_source.reference_source_selector")
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69 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
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70 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
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71 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
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72 #else
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73 --REFERENCE_SEQUENCE $getVar($sect + "reference_source.reference_sequence")
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74 #end if
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75 #end if
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76 #end if
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77 #end for
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78 </template>
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79
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80 <template name="picard_ref_opts_plain">
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81 #for $sect in $sections
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82 #if $varExists($sect + "reference_source.reference_source_selector")
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83 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
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84 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
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85 --REFERENCE $getVar($sect + "reference_source.reference_sequence.fields.path")
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86 #else
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87 --REFERENCE $getVar($sect + "reference_source.reference_sequence")
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88 #end if
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89 #end if
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90 #end if
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91 #end for
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92 </template>
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93
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94 <template name="ref_opts_input">
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95 #for $sect in $sections
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96 #if $varExists($sect + "reference_source.reference_source_selector")
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97 #if $getVar($sect + "reference_source.reference_source_selector") != "no_ref"
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98 #if $getVar($sect + "reference_source.reference_source_selector") != "history"
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99 --input $getVar($sect + "reference_source.reference_sequence.fields.path")
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100 #else
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101 --input $getVar($sect + "reference_source.reference_sequence")
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102 #end if
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103 #end if
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104 #end if
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105 #end for
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106 </template>
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107
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108
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109 <!--Interval Macros-->
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110 <template name="gatk_ints_chth">
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111 #for $sect in $sections
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112 #if $varExists($sect + "ival_type.ival_type_sel")
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113 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
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114 #if $varExists($sect + "ival_type.intervals")
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115 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
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116 --intervals intervals.interval_list
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117 #end if
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118 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
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119 --intervals intervals.bed
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120 #end if
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121 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
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122 --intervals intervals.vcf
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123 #end if
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124 #end if
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125 #else
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126 #if $varExists($sect + "ival_type.intervals")
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127 --intervals $getVar($sect + "ival_type.intervals")
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128 #end if
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129 #end if
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130 #if $varExists($sect + "ival_type.interval_padding")
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131 --interval-padding $getVar($sect + "ival_type.interval_padding")
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132 #end if
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133 #end if
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134 #end for
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135 </template>
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136
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137
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138 <template name="pre_gatk_ints_chth"><![CDATA[
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139 #for $sect in $sections
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140 #if $varExists($sect + "ival_type.ival_type_sel")
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141 #if $getVar($sect + "ival_type.ival_type_sel") == "ival_file"
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142 #if $varExists($sect + "ival_type.intervals")
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143 #if $getVar($sect + "ival_type.intervals").is_of_type("gatk_interval")
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144 ln -s $getVar($sect + "ival_type.intervals") intervals.interval_list &&
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145 #end if
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146 #if $getVar($sect + "ival_type.intervals").is_of_type("bed")
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147 ln -s $getVar($sect + "ival_type.intervals") intervals.bed &&
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148 #end if
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149 #if $getVar($sect + "ival_type.intervals").is_of_type("vcf")
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150 ln -s $getVar($sect + "ival_type.intervals") intervals.vcf &&
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151 #end if
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152 #end if
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153 #end if
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154 #end if
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155 #end for
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156 ]]></template>
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157
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158 <xml name="gatk_ints">
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159 <conditional name="ival_type">
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160 <param name="ival_type_sel" type="select" label="Choose Genomic Interval Source">
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161 <option value="ival_file" selected="true">Interval File</option>
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162 <option value="ival_text" selected="false">Interval Text Input</option>
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163 </param>
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164 <when value="ival_file">
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165 <param name="intervals" argument="--intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Intervals File" help="One or more genomic intervals over which to operate"/>
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166 <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
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167 </when>
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168 <when value="ival_text">
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169 <param name="intervals" argument="--intervals" type="text" optional="true" label="Intervals Text Input" help="One or more genomic intervals over which to operate. Enter in chrom:start-stop format."/>
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170 <param name="interval_padding" argument="--interval-padding" type="integer" optional="true" value="0" label="Interval Padding" help="Amount of padding (in bp) to add to each interval you are including."/>
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171 </when>
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172 </conditional>
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173 </xml>
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174
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175
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176 <!--Exclude Intervals-->
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177 <xml name="gatk_excl_ints">
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178 <conditional name="excl_ival_type">
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179 <param name="excl_ival_type_sel" type="select" label="Choose Genomic Interval Exclusion Source">
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180 <option value="excl_ival_file" selected="true">Exclude Interval File</option>
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181 <option value="excl_ival_text" selected="false">Exclude Interval Text Input</option>
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182 </param>
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183 <when value="excl_ival_file">
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184 <param name="exclude_intervals" argument="--exclude-intervals" type="data" optional="true" format="bed,vcf,gatk_interval" label="Exclude Intervals File" help="One or more genomic intervals to exclude from processing"/>
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185 <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
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186 </when>
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187 <when value="excl_ival_text">
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188 <param name="exclude_intervals" argument="--exclude-intervals" type="text" optional="true" label="Exclude Intervals Text Input" help="One or more genomic intervals to exclude from processing. Enter in chrom:start-stop format."/>
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189 <param name="interval_exclusion_padding" argument="--interval-exclusion-padding" type="integer" optional="true" value="0" label="Interval Exclusion Padding" help="Amount of padding (in bp) to add to each interval you are excluding."/>
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190 </when>
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191 </conditional>
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192 </xml>
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193
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194 <template name="gatk_excl_ints_chth">
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195 #for $sect in $sections
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196 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
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197 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "ival_file"
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198 #if $varExists($sect + "excl_ival_type.exclude_intervals")
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199 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
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200 --exclude-intervals excl_intervals.interval_list
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201 #end if
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dave
parents:
diff changeset
202 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
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dave
parents:
diff changeset
203 --exclude-intervals excl_intervals.bed
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dave
parents:
diff changeset
204 #end if
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dave
parents:
diff changeset
205 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
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dave
parents:
diff changeset
206 --exclude-intervals excl_intervals.vcf
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dave
parents:
diff changeset
207 #end if
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dave
parents:
diff changeset
208 #end if
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dave
parents:
diff changeset
209 #elif $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_text"
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dave
parents:
diff changeset
210 #if $varExists($sect + "excl_ival_type.exclude_intervals")
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dave
parents:
diff changeset
211 --exclude-intervals $getVar($sect + "excl_ival_type.exclude_intervals")
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dave
parents:
diff changeset
212 #end if
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dave
parents:
diff changeset
213 #else
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dave
parents:
diff changeset
214 #pass
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dave
parents:
diff changeset
215 #end if
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dave
parents:
diff changeset
216 #if $varExists($sect + "excl_ival_type.interval_exclusion_padding")
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dave
parents:
diff changeset
217 --interval-exclusion-padding $getVar($sect + "excl_ival_type.interval_exclusion_padding")
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dave
parents:
diff changeset
218 #end if
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dave
parents:
diff changeset
219 #end if
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dave
parents:
diff changeset
220 #end for
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dave
parents:
diff changeset
221 </template>
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dave
parents:
diff changeset
222
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dave
parents:
diff changeset
223 <template name="pre_gatk_excl_ints_chth"><![CDATA[
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dave
parents:
diff changeset
224 #for $sect in $sections
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dave
parents:
diff changeset
225 #if $varExists($sect + "excl_ival_type.excl_ival_type_sel")
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dave
parents:
diff changeset
226 #if $getVar($sect + "excl_ival_type.excl_ival_type_sel") == "excl_ival_file"
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dave
parents:
diff changeset
227 #if $varExists($sect + "excl_ival_type.exclude_intervals")
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dave
parents:
diff changeset
228 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("gatk_interval")
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dave
parents:
diff changeset
229 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.interval_list &&
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dave
parents:
diff changeset
230 #end if
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dave
parents:
diff changeset
231 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("bed")
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dave
parents:
diff changeset
232 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.bed &&
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dave
parents:
diff changeset
233 #end if
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dave
parents:
diff changeset
234 #if $getVar($sect + "excl_ival_type.exclude_intervals").is_of_type("vcf")
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dave
parents:
diff changeset
235 ln -s $getVar($sect + "excl_ival_type.exclude_intervals") excl_intervals.vcf &&
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dave
parents:
diff changeset
236 #end if
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dave
parents:
diff changeset
237 #end if
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dave
parents:
diff changeset
238 #end if
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dave
parents:
diff changeset
239 #end if
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dave
parents:
diff changeset
240 #end for
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dave
parents:
diff changeset
241 ]]></template>
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dave
parents:
diff changeset
242
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dave
parents:
diff changeset
243 <!--Sequence dictionary selection options for Picard type tools-->
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dave
parents:
diff changeset
244 <template name="picard_seqdict_opts">
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dave
parents:
diff changeset
245 #for $sect in $sections
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dave
parents:
diff changeset
246 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
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dave
parents:
diff changeset
247 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
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dave
parents:
diff changeset
248 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
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dave
parents:
diff changeset
249 #set seq_dict_loc = ''.join($getVar($sect + seqdict_source.seqdict_sequence).fields.path.split('.')[:-1]) + '.dict'
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dave
parents:
diff changeset
250 --SEQUENCE_DICTIONARY $seq_dict_loc
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dave
parents:
diff changeset
251 #else
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dave
parents:
diff changeset
252 --SEQUENCE_DICTIONARY $getVar($sect + "seqdict_source.seqdict_sequence")
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dave
parents:
diff changeset
253 #end if
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dave
parents:
diff changeset
254 #end if
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dave
parents:
diff changeset
255 #end if
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dave
parents:
diff changeset
256 #end for
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dave
parents:
diff changeset
257 </template>
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dave
parents:
diff changeset
258
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dave
parents:
diff changeset
259 <template name="gatk_seqdict">
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dave
parents:
diff changeset
260 #for $sect in $sections
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dave
parents:
diff changeset
261 #if $varExists($sect + "seqdict_source.seqdict_source_selector")
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dave
parents:
diff changeset
262 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "no_seq_dict"
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dave
parents:
diff changeset
263 #if $getVar($sect + "seqdict_source.seqdict_source_selector") != "history"
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dave
parents:
diff changeset
264 #set $seq_dict_loc = ''.join($getVar($sect + "seqdict_source.seqdict_sequence").fields.path.split('.')[:-1]) + '.dict'
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dave
parents:
diff changeset
265 --sequence-dictionary $seq_dict_loc
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dave
parents:
diff changeset
266 #else
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dave
parents:
diff changeset
267 --sequence-dictionary $getVar($sect + "seqdict_source.seqdict_sequence")
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dave
parents:
diff changeset
268 #end if
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dave
parents:
diff changeset
269 #end if
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dave
parents:
diff changeset
270 #end if
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dave
parents:
diff changeset
271 #end for
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dave
parents:
diff changeset
272 </template>
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dave
parents:
diff changeset
273
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dave
parents:
diff changeset
274 <xml name="seq_dict_sel">
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dave
parents:
diff changeset
275 <conditional name="seqdict_source">
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dave
parents:
diff changeset
276 <param name="seqdict_source_selector" type="select" label="Choose the source for the sequence dictionary">
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dave
parents:
diff changeset
277 <option value="cached">Locally cached</option>
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dave
parents:
diff changeset
278 <option value="history">History</option>
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dave
parents:
diff changeset
279 <option value="no_seq_dict" selected="true">Do not pass</option>
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dave
parents:
diff changeset
280 </param>
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dave
parents:
diff changeset
281 <when value="cached">
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dave
parents:
diff changeset
282 <param name="seqdict_sequence" type="select" label="Sequence Dictionary" help="Sequence dictionary file." >
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dave
parents:
diff changeset
283 <options from_data_table="all_fasta" >
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dave
parents:
diff changeset
284 <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
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dave
parents:
diff changeset
285 </options>
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dave
parents:
diff changeset
286 </param>
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dave
parents:
diff changeset
287 </when>
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dave
parents:
diff changeset
288 <when value="history">
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dave
parents:
diff changeset
289 <param name="seqdict_sequence" type="data" format="txt" label="Sequence Dictionary" help="Sequence dictionary file. Must be in dict format." />
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dave
parents:
diff changeset
290 </when>
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dave
parents:
diff changeset
291 <when value="no_seq_dict" />
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dave
parents:
diff changeset
292 </conditional>
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dave
parents:
diff changeset
293 </xml>
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dave
parents:
diff changeset
294
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dave
parents:
diff changeset
295 <!--BAM input-->
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dave
parents:
diff changeset
296 <template name="picard_bam_input">
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dave
parents:
diff changeset
297 --INPUT input.bam
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dave
parents:
diff changeset
298 </template>
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dave
parents:
diff changeset
299
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dave
parents:
diff changeset
300 <template name="gatk_bam_input">
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dave
parents:
diff changeset
301 --input input.bam
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dave
parents:
diff changeset
302 </template>
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dave
parents:
diff changeset
303
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dave
parents:
diff changeset
304 <template name="bam_index_pre_chth"><![CDATA[
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dave
parents:
diff changeset
305 #for $sect in $sections
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dave
parents:
diff changeset
306 #if $varExists($sect + "input")
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dave
parents:
diff changeset
307 #if $getVar($sect + "input").is_of_type("bam")
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dave
parents:
diff changeset
308 ln -s $getVar($sect + "input") input.bam &&
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dave
parents:
diff changeset
309 samtools index input.bam &&
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dave
parents:
diff changeset
310 #else
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dave
parents:
diff changeset
311 ln -s $getVar($sect + "input") input.sam &&
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dave
parents:
diff changeset
312 samtools view -bS input.sam -o input.bam &&
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dave
parents:
diff changeset
313 samtools index input.bam &&
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dave
parents:
diff changeset
314 #end if
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dave
parents:
diff changeset
315 #end if
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dave
parents:
diff changeset
316 #end for
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dave
parents:
diff changeset
317 ]]></template>
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dave
parents:
diff changeset
318
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dave
parents:
diff changeset
319 <xml name="gatk_bam_req_params">
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dave
parents:
diff changeset
320 <param argument="--input" type="data" format="bam,sam" label="Input BAM/SAM/CRAM file" />
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dave
parents:
diff changeset
321 </xml>
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dave
parents:
diff changeset
322
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dave
parents:
diff changeset
323 <template name="picard_bam_index"><![CDATA[
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dave
parents:
diff changeset
324 #if $input.is_of_type("bam")
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dave
parents:
diff changeset
325 ln -s $INPUT input.bam &&
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dave
parents:
diff changeset
326 samtools index input.bam &&
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dave
parents:
diff changeset
327 #else
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dave
parents:
diff changeset
328 ln -s $INPUT input.sam &&
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dave
parents:
diff changeset
329 samtools view -bS input.sam -o input.bam &&
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dave
parents:
diff changeset
330 samtools index input.bam &&
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dave
parents:
diff changeset
331 #end if
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dave
parents:
diff changeset
332 ]]></template>
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dave
parents:
diff changeset
333
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dave
parents:
diff changeset
334
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dave
parents:
diff changeset
335 <!--Output goes to stdout, no output parameter exists.-->
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dave
parents:
diff changeset
336 <template name="stdout_to_output">
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dave
parents:
diff changeset
337 > output.txt
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dave
parents:
diff changeset
338 </template>
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dave
parents:
diff changeset
339
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dave
parents:
diff changeset
340 <xml name="stdout_to_output_params">
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dave
parents:
diff changeset
341 <data format="txt" name="output" label="${tool.name} on ${on_string}: txt" from_work_dir="output.txt" />
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dave
parents:
diff changeset
342 </xml>
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dave
parents:
diff changeset
343
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dave
parents:
diff changeset
344 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
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dave
parents:
diff changeset
345 <template name="gatk_input_multi"><![CDATA[
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dave
parents:
diff changeset
346 #for $num, $file in enumerate($variant)
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dave
parents:
diff changeset
347 #if $file.is_of_type("vcf_bgzip")
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dave
parents:
diff changeset
348 --variant input${num}.vcf.gz
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dave
parents:
diff changeset
349 #elif $file.is_of_type("txt")
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dave
parents:
diff changeset
350 --variant input${num}.list
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dave
parents:
diff changeset
351 #else
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dave
parents:
diff changeset
352 --variant input${num}.vcf
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dave
parents:
diff changeset
353 #end if
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dave
parents:
diff changeset
354 #end for
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dave
parents:
diff changeset
355 ]]></template>
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dave
parents:
diff changeset
356
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dave
parents:
diff changeset
357 <!--Multiple input files, true for List[File] types, and sometimes List[String] types -->
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dave
parents:
diff changeset
358 <template name="gatk_input_single"><![CDATA[
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dave
parents:
diff changeset
359 #if $variant.is_of_type("vcf_bgzip")
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dave
parents:
diff changeset
360 --variant input${num}.vcf.gz
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dave
parents:
diff changeset
361 #elif $variant.is_of_type("txt")
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dave
parents:
diff changeset
362 --variant input${num}.list
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dave
parents:
diff changeset
363 #else
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dave
parents:
diff changeset
364 --variant input${num}.vcf
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dave
parents:
diff changeset
365 #end if
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dave
parents:
diff changeset
366 ]]></template>
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dave
parents:
diff changeset
367
c27f4eb641bf Uploaded
dave
parents:
diff changeset
368 <template name="gatk_tabix_multi"><![CDATA[
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dave
parents:
diff changeset
369 #for $num, $file in enumerate($variant)
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dave
parents:
diff changeset
370 #set datatype = $file.datatype
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dave
parents:
diff changeset
371 #if $file.is_of_type("vcf_bgzip")
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dave
parents:
diff changeset
372 ln -s $file input${num}.vcf.gz &&
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dave
parents:
diff changeset
373 tabix input${num}.vcf.gz &&
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dave
parents:
diff changeset
374 #elif $file.is_of_type("txt")
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dave
parents:
diff changeset
375 ln -s $file input${num}.list &&
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dave
parents:
diff changeset
376 #else
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dave
parents:
diff changeset
377 ln -s $file input${num}.vcf &&
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dave
parents:
diff changeset
378 #end if
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dave
parents:
diff changeset
379 #end for
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dave
parents:
diff changeset
380 ]]></template>
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dave
parents:
diff changeset
381
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dave
parents:
diff changeset
382 <xml name="vcf_input_params_multi">
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dave
parents:
diff changeset
383 <param name="input" type="data" multiple="true" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/>
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dave
parents:
diff changeset
384 </xml>
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dave
parents:
diff changeset
385
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dave
parents:
diff changeset
386
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dave
parents:
diff changeset
387
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dave
parents:
diff changeset
388 <!--ABOVE HAS BEEN REVIEWED-->
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dave
parents:
diff changeset
389
c27f4eb641bf Uploaded
dave
parents:
diff changeset
390
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dave
parents:
diff changeset
391
c27f4eb641bf Uploaded
dave
parents:
diff changeset
392
c27f4eb641bf Uploaded
dave
parents:
diff changeset
393
c27f4eb641bf Uploaded
dave
parents:
diff changeset
394
c27f4eb641bf Uploaded
dave
parents:
diff changeset
395
c27f4eb641bf Uploaded
dave
parents:
diff changeset
396
c27f4eb641bf Uploaded
dave
parents:
diff changeset
397
c27f4eb641bf Uploaded
dave
parents:
diff changeset
398
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dave
parents:
diff changeset
399 <!--{-->
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dave
parents:
diff changeset
400 <!--"summary": "BAM/SAM/CRAM file containing reads",-->
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dave
parents:
diff changeset
401 <!--"name": "&#45;&#45;input",-->
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dave
parents:
diff changeset
402 <!--"synonyms": "-I",-->
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dave
parents:
diff changeset
403 <!--"type": "List[String]",-->
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dave
parents:
diff changeset
404 <!--"required": "yes",-->
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dave
parents:
diff changeset
405 <!--"fulltext": "",-->
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dave
parents:
diff changeset
406 <!--"defaultValue": "[]",-->
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dave
parents:
diff changeset
407 <!--"minValue": "NA",-->
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dave
parents:
diff changeset
408 <!--"maxValue": "NA",-->
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dave
parents:
diff changeset
409 <!--"minRecValue": "NA",-->
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dave
parents:
diff changeset
410 <!--"maxRecValue": "NA",-->
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dave
parents:
diff changeset
411 <!--"kind": "required",-->
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dave
parents:
diff changeset
412 <!--"options": []-->
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dave
parents:
diff changeset
413 <!--},-->
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dave
parents:
diff changeset
414 <!--Required BAM input, GATK tool, may be specified multiple times.-->
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dave
parents:
diff changeset
415 <!--BAM should be indexed on the fly.-->
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dave
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diff changeset
416 <!--Parameter is required, so is not contained within a section.-->
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dave
parents:
diff changeset
417 <!--Only decriptor that makes this unique for all input parameters is the summary field.-->
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dave
parents:
diff changeset
418 <!--{'pre_chth': ['bam_index_pre_chth'],-->
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dave
parents:
diff changeset
419 <!--'main_chth': ['picard_bam_input'],-->
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dave
parents:
diff changeset
420 <!--'main_xml': ['gatk_bam_req_params']}},-->
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dave
parents:
diff changeset
421
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dave
parents:
diff changeset
422
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dave
parents:
diff changeset
423
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dave
parents:
diff changeset
424
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dave
parents:
diff changeset
425
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dave
parents:
diff changeset
426
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dave
parents:
diff changeset
427
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dave
parents:
diff changeset
428
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dave
parents:
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429
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dave
parents:
diff changeset
430
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dave
parents:
diff changeset
431
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dave
parents:
diff changeset
432
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dave
parents:
diff changeset
433
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dave
parents:
diff changeset
434 <!--Macros for multiple input tools. List[File] in GATK json.-->
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dave
parents:
diff changeset
435 <template name="vcf_tabix_multi"><![CDATA[
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dave
parents:
diff changeset
436 #for $num, $file in enumerate($input)
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parents:
diff changeset
437 #set datatype = $file.datatype
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dave
parents:
diff changeset
438 #if $file.is_of_type("vcf_bgzip")
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dave
parents:
diff changeset
439 ln -s $file input${num}.vcf.gz &&
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dave
parents:
diff changeset
440 tabix input${num}.vcf.gz &&
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dave
parents:
diff changeset
441 #else
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dave
parents:
diff changeset
442 ln -s $file input${num}.vcf &&
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parents:
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443 #end if
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parents:
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444 #end for
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parents:
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445 ]]></template>
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dave
parents:
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446
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dave
parents:
diff changeset
447 <template name="vcf_input_multi_picard"><![CDATA[
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dave
parents:
diff changeset
448 #for $num, $file in enumerate($input)
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parents:
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449 #if $file.is_of_type("vcf_bgzip")
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parents:
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450 --INPUT input${num}.vcf.gz
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parents:
diff changeset
451 #else
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parents:
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452 --INPUT input${num}.vcf
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453 #end if
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parents:
diff changeset
454 #end for
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parents:
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455 ]]></template>
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dave
parents:
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456
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dave
parents:
diff changeset
457 <template name="vcf_input_multi"><![CDATA[
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parents:
diff changeset
458 #for $num, $file in enumerate($input)
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dave
parents:
diff changeset
459 #if $file.is_of_type("vcf_bgzip")
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dave
parents:
diff changeset
460 --input input${num}.vcf.gz
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dave
parents:
diff changeset
461 #else
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parents:
diff changeset
462 --input input${num}.vcf
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parents:
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463 #end if
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parents:
diff changeset
464 #end for
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parents:
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465 ]]></template>
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parents:
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466
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dave
parents:
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467
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parents:
diff changeset
468 <!--Picard single input tools-->
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dave
parents:
diff changeset
469 <template name="vcf_tabix"><![CDATA[
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parents:
diff changeset
470 #set datatype = $input.datatype
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parents:
diff changeset
471 #if $input.is_of_type("vcf_bgzip")
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parents:
diff changeset
472 ln -s $input input.vcf.gz &&
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dave
parents:
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473 tabix input.vcf.gz &&
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dave
parents:
diff changeset
474 #else
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dave
parents:
diff changeset
475 ln -s $input input.vcf &&
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parents:
diff changeset
476 #end if
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parents:
diff changeset
477 ]]></template>
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dave
parents:
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478
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dave
parents:
diff changeset
479 <template name="gatk_tabix"><![CDATA[
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parents:
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480 #set datatype = $variant.datatype
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dave
parents:
diff changeset
481 #if $variant.is_of_type("vcf_bgzip")
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dave
parents:
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482 ln -s $variant input.vcf.gz &&
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dave
parents:
diff changeset
483 tabix input.vcf.gz &&
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dave
parents:
diff changeset
484 #else
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dave
parents:
diff changeset
485 ln -s $variant input.vcf &&
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dave
parents:
diff changeset
486 gatk IndexFeatureFile -F input.vcf &&
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parents:
diff changeset
487 #end if
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parents:
diff changeset
488 ]]></template>
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dave
parents:
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489
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dave
parents:
diff changeset
490 <template name="vcf_input_picard"><![CDATA[
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parents:
diff changeset
491 #if $input.is_of_type("vcf_bgzip")
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parents:
diff changeset
492 --INPUT input.vcf.gz
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parents:
diff changeset
493 #else
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parents:
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494 --INPUT input.vcf
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parents:
diff changeset
495 #end if
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parents:
diff changeset
496 ]]></template>
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dave
parents:
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497
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dave
parents:
diff changeset
498 <template name="vcf_input"><![CDATA[
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dave
parents:
diff changeset
499 #if $input.is_of_type("vcf_bgzip")
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dave
parents:
diff changeset
500 --input input.vcf.gz
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parents:
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501 #else
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parents:
diff changeset
502 --input input.vcf
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parents:
diff changeset
503 #end if
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parents:
diff changeset
504 ]]></template>
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dave
parents:
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505
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dave
parents:
diff changeset
506 <template name="gatk_input"><![CDATA[
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dave
parents:
diff changeset
507 #if $variant.is_of_type("vcf_bgzip")
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parents:
diff changeset
508 --variant input.vcf.gz
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dave
parents:
diff changeset
509 #else
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parents:
diff changeset
510 --variant input.vcf
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parents:
diff changeset
511 #end if
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parents:
diff changeset
512 ]]></template>
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parents:
diff changeset
513
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dave
parents:
diff changeset
514 <template name="gatk_gvcf_tabix"><![CDATA[
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dave
parents:
diff changeset
515 #if $variant
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parents:
diff changeset
516 ln -s $variant input.g.vcf &&
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parents:
diff changeset
517 #end if
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parents:
diff changeset
518 ]]></template>
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dave
parents:
diff changeset
519
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dave
parents:
diff changeset
520 <template name="gatk_gvcf_input"><![CDATA[
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dave
parents:
diff changeset
521 --variant input.g.vcf
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parents:
diff changeset
522 ]]></template>
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dave
parents:
diff changeset
523
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dave
parents:
diff changeset
524 <xml name="gatk_gvcf_input_params">
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dave
parents:
diff changeset
525 <param name="variant" type="data" multiple="false" format="vcf" label="Input gVCF file" help=""/>
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dave
parents:
diff changeset
526 </xml>
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dave
parents:
diff changeset
527
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dave
parents:
diff changeset
528 <xml name="vcf_input_params">
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parents:
diff changeset
529 <param name="input" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="Input VCF(s) to be sorted. Multiple inputs must have the same sample names (in order)"/>
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parents:
diff changeset
530 </xml>
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parents:
diff changeset
531
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dave
parents:
diff changeset
532 <xml name="gatk_vcf_input_params">
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dave
parents:
diff changeset
533 <param name="variant" type="data" multiple="false" format="vcf,vcf_bgzip" label="Input VCF file" help="A VCF file containing variants."/>
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parents:
diff changeset
534 </xml>
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dave
parents:
diff changeset
535
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dave
parents:
diff changeset
536 <xml name="gatk_vcf_input_params_multi">
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dave
parents:
diff changeset
537 <param name="variant" type="data" multiple="true" format="vcf,vcf_bgzip,txt" label="Input VCF file(s)" help="A VCF file containing variants or a list of VCFs. Can be specified multiple times."/>
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parents:
diff changeset
538 </xml>
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dave
parents:
diff changeset
539
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dave
parents:
diff changeset
540 <xml name="gatk_req_params">
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dave
parents:
diff changeset
541 <param name="input" type="data" format="bam,sam,cram" label="Input BAM/SAM/CRAM file" />
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dave
parents:
diff changeset
542 </xml>
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dave
parents:
diff changeset
543
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dave
parents:
diff changeset
544 <!--HDF5 Inputs-->
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dave
parents:
diff changeset
545
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dave
parents:
diff changeset
546 <xml name="hdf5_input">
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dave
parents:
diff changeset
547 <param name="input" type="data" format="h5,tabular" label="Input TSV or HDF5" help="Input TSV or HDF5 file containing integer read counts in genomic intervals for a single case sample (output of CollectReadCounts)." />
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parents:
diff changeset
548 </xml>
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dave
parents:
diff changeset
549
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dave
parents:
diff changeset
550 <template name="hdf5_input_chth"><![CDATA[
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dave
parents:
diff changeset
551 --input "${input}"
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dave
parents:
diff changeset
552 ]]></template>
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dave
parents:
diff changeset
553
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dave
parents:
diff changeset
554 <template name="hdf5_output_chth">
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dave
parents:
diff changeset
555 --output "${output}"
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dave
parents:
diff changeset
556 </template>
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dave
parents:
diff changeset
557
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dave
parents:
diff changeset
558 <xml name="hdf5_output">
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dave
parents:
diff changeset
559 <data format="h5" name="output" label="${tool.name} on ${on_string}: HDF5" help="Output file for read counts." />
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dave
parents:
diff changeset
560 </xml>
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dave
parents:
diff changeset
561
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dave
parents:
diff changeset
562 <!--Output specific to ModelSegments. Files created based on prefix, so force that to be what we want, then pull important files with from_work_dir.-->
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dave
parents:
diff changeset
563 <!--${SAMPLE}.cr.seg-->
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dave
parents:
diff changeset
564 <!--${SAMPLE}.modelFinal.seg-->
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dave
parents:
diff changeset
565 <template name="modelsegments_chth"><![CDATA[
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dave
parents:
diff changeset
566 --output "."
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dave
parents:
diff changeset
567 --output-prefix "modelsegments"
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dave
parents:
diff changeset
568 ]]></template>
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dave
parents:
diff changeset
569
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dave
parents:
diff changeset
570 <xml name="modelsegments_output">
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dave
parents:
diff changeset
571 <data format="tabular" name="cr_seg" label="${tool.name} on ${on_string}: cr.seg" help="Copy-ratio segments." from_work_dir="modelsegments.cr.seg"/>
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dave
parents:
diff changeset
572 <data format="tabular" name="modelfinal_seg" label="${tool.name} on ${on_string}: modelFinal.seg" help="Modeled Segments" from_work_dir="modelsegments.modelFinal.seg"/>
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parents:
diff changeset
573 </xml>
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dave
parents:
diff changeset
574
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dave
parents:
diff changeset
575 <!--deltaMAD.txt-->
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dave
parents:
diff changeset
576 <!--denoisedLimit4.png-->
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dave
parents:
diff changeset
577 <!--denoisedMAD.txt-->
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dave
parents:
diff changeset
578 <!--denoised.png-->
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dave
parents:
diff changeset
579 <!--scaledDeltaMAD.txt-->
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dave
parents:
diff changeset
580 <!--modeled.png-->
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dave
parents:
diff changeset
581 <!--standardizedMAD.txt-->
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dave
parents:
diff changeset
582
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dave
parents:
diff changeset
583 <template name="plotmodeledsegments_chth"><![CDATA[
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dave
parents:
diff changeset
584 --output "."
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dave
parents:
diff changeset
585 --output-prefix "plotmodeledsegments"
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dave
parents:
diff changeset
586 ]]></template>
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dave
parents:
diff changeset
587
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dave
parents:
diff changeset
588 <xml name="plotmodeledsegments_output">
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dave
parents:
diff changeset
589 <data format="png" name="modeled_png" label="${tool.name} on ${on_string}: modeled.png" help="Copy-Ratio Plot" from_work_dir="plotmodeledsegments.modeled.png"/>
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dave
parents:
diff changeset
590 </xml>
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dave
parents:
diff changeset
591
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dave
parents:
diff changeset
592 <!--Common Picard options-->
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dave
parents:
diff changeset
593 <template name="picard_opts">
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dave
parents:
diff changeset
594 #if $picard_adv.arguments_file
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dave
parents:
diff changeset
595 --arguments_file ${picard_adv.arguments_file}
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dave
parents:
diff changeset
596 #end if
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dave
parents:
diff changeset
597 --COMPRESSION_LEVEL ${picard_adv.COMPRESSION_LEVEL}
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dave
parents:
diff changeset
598 #if $picard_adv.GA4GH_CLIENT_SECRETS
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dave
parents:
diff changeset
599 --GA4GH_CLIENT_SECRETS ${picard_adv.GA4GH_CLIENT_SECRETS}
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dave
parents:
diff changeset
600 #end if
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dave
parents:
diff changeset
601 --MAX_RECORDS_IN_RAM ${picard_adv.MAX_RECORDS_IN_RAM}
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dave
parents:
diff changeset
602 --VALIDATION_STRINGENCY ${picard_adv.VALIDATION_STRINGENCY}
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dave
parents:
diff changeset
603 --VERBOSITY ${picard_adv.VERBOSITY}
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dave
parents:
diff changeset
604 ${picard_adv.CREATE_MD5_FILE}
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dave
parents:
diff changeset
605 ${picard_adv.USE_JDK_DEFLATER}
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dave
parents:
diff changeset
606 ${picard_adv.USE_JDK_INFLATER}
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dave
parents:
diff changeset
607 </template>
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dave
parents:
diff changeset
608
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dave
parents:
diff changeset
609 <xml name="picard_params">
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dave
parents:
diff changeset
610 <section name="picard_adv" title="Advanced Picard Options (Only change these if you know what you're doing.)" expanded="False">
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dave
parents:
diff changeset
611 <param argument="--arguments_file" type="data" optional="true" format="txt" label="Arguments File" help="read one or more arguments files and add them to the command line" />
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dave
parents:
diff changeset
612 <param argument="--COMPRESSION_LEVEL" type="integer" optional="true" value="5" min="1" max="9" label="Compression Level" help="Compression level for all compressed files created (e.g. BAM and VCF)." />
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dave
parents:
diff changeset
613 <param argument="--CREATE_MD5_FILE" truevalue="--CREATE_MD5_FILE" falsevalue="" type="boolean" optional="true" checked="false" label="Create MD5 File" help="Whether to create an MD5 digest for any BAM or FASTQ files created." />
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dave
parents:
diff changeset
614 <param argument="--GA4GH_CLIENT_SECRETS" type="data" format="json" optional="true" label="Ga4Gh Client Secrets" help="Google Genomics API client_secrets.json file path." />
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dave
parents:
diff changeset
615 <param argument="--MAX_RECORDS_IN_RAM" type="integer" optional="true" value="500000" label="Max Records In Ram" help="When writing files that need to be sorted, this will specify the number of records stored in RAM before spilling to disk. Increasing this number reduces the number of file handles needed to sort the file, and increases the amount of RAM needed." />
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parents:
diff changeset
616 <param argument="--TMP_DIR" type="text" optional="true" label="Tmp Dir" help="One or more directories with space available to be used by this program for temporary storage of working files. Keep in mind, you must be able to access this directory from either your user, or from the Galaxy user, depending on your configuration." />
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parents:
diff changeset
617 <param argument="--USE_JDK_DEFLATER" truevalue="--USE_JDK_DEFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Deflater" help="Use the JDK Deflater instead of the Intel Deflater for writing compressed output" />
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parents:
diff changeset
618 <param argument="--USE_JDK_INFLATER" truevalue="--USE_JDK_INFLATER" falsevalue="" type="boolean" optional="true" checked="false" label="Use Jdk Inflater" help="Use the JDK Inflater instead of the Intel Inflater for reading compressed input" />
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619 <param argument="--VALIDATION_STRINGENCY" type="select" optional="true" label="Validation Stringency" help="Validation stringency for all SAM files read by this program. Setting stringency to SILENT can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) do not otherwise need to be decoded." >
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620 <option value="STRICT" selected="true">STRICT</option>
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621 <option value="LENIENT" selected="false">LENIENT</option>
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622 <option value="SILENT" selected="false">SILENT</option>
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623 </param>
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624 <param argument="--VERBOSITY" type="select" optional="true" label="Verbosity" help="Control verbosity of logging." >
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625 <option value="ERROR" selected="false">ERROR</option>
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626 <option value="WARNING" selected="false">WARNING</option>
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627 <option value="INFO" selected="true">INFO</option>
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628 <option value="DEBUG" selected="false">DEBUG</option>
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629 </param>
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630 </section>
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631 </xml>
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632
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633 <!--Provides option to create gzipped output for VCF files-->
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634 <xml name="gzip_vcf_params">
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635 <param name="gzipped_output" type="boolean" checked="true" label="GZIP Output?" help="If you would like gzipped output, check this box. In general, it would be preferable to do this, unless your downstream tool does not support handling of gzipped files." />
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636 </xml>
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637
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638 <!--Output related Picard options-->
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639 <xml name="gzip_vcf_output_params">
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640 <data format="vcf" name="output_vcf" label="${tool.name} on ${on_string}: vcf" from_work_dir="output.vcf" >
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641 <filter>not gzipped_output</filter>
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642 </data>
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643 <data format="vcf_bgzip" name="output_vcf_bgzip" label="${tool.name} on ${on_string}: vcf_bgzip" from_work_dir="output.vcf.gz" >
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644 <filter>gzipped_output</filter>
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645 </data>
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646 </xml>
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647
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648
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649 <!--These are the same, other than the capitalization of output, so maybe a better way to do this.-->
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650 <template name="picard_vcf_output_opts">
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651 #if $gzipped_output
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652 --OUTPUT output.vcf.gz
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653 #else
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654 --OUTPUT output.vcf
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655 #end if
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656 </template>
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657
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658 <template name="vcf_output_opts">
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659 #if $gzipped_output
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660 --output output.vcf.gz
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661 #else
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662 --output output.vcf
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663 #end if
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664 </template>
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665
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666 <xml name="picard_output_params">
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667 <data format="txt" name="output_md5" label="${tool.name} on ${on_string}: md5sum(txt)" from_work_dir="output.bam.md5" >
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668 <filter>picard_adv['CREATE_MD5_FILE']</filter>
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669 </data>
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670 </xml>
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671
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672
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673 <!--<template name="ref_opts">-->
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674 <!--#set $sections = ['optional','advanced','common','deprecated','']-->
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675 <!--#silent $sys.stderr.write("I WOULD LIKE TO SHOW THE SECTION VARIABLE: '${sections}'\n")-->
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676 <!--#for $sect in $sections-->
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677 <!--#if $varExists('$sect.reference_source.reference_source_selector')-->
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678 <!--#if $sect.reference_source.reference_source_selector != "no_ref"-->
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679 <!--#if $sect.reference_source.reference_source_selector != "history"-->
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680 <!--&#45;&#45;reference ${sect.reference_source.reference_sequence.fields.path}-->
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681 <!--#else-->
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682 <!--&#45;&#45;reference ${sect.reference_source.reference_sequence}-->
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683 <!--#end if-->
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684 <!--#end if-->
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685 <!--#end if-->
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686 <!--#end for-->
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687 <!--</template>-->
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688
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689
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690 <!--<template name="ref_opts_opt">-->
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691 <!--#if $optional.reference_source.reference_source_selector != "no_ref"-->
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692 <!--#if $optional.reference_source.reference_source_selector != "history"-->
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693 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence.fields.path}-->
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694 <!--#else-->
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695 <!--&#45;&#45;reference ${optional.reference_source.reference_sequence}-->
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696 <!--#end if-->
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697 <!--#end if-->
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698 <!--</template>-->
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699
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700
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701 <!--Citations-->
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702 <xml name="citations">
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703 <citation type="doi">10.1101/gr.107524.110</citation>
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704 <citation type="doi">10.1038/ng.806</citation>
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705 <citation type="doi">10.1002/0471250953.bi1110s43</citation>
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706 <citation type="doi">10.1101/201178</citation>
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707 <yield />
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708 </xml>
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709
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710 </macros>