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1 <tool id="pl_listuniquevariants" name="List_Unique_Variants" version="0.0.1">
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2
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3 <description>with annotations from gene or var files</description> <!--adds description in toolbar-->
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4
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5 <command interpreter="perl"> <!--run executable-->
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6 #if $file_types.file_type =="var2"
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7 List_Unique_Variants_2_1_0.pl --File_Type V --Output_File $output
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8 --Var_Type $file_types.variants
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9 $file_types.scoresVAF
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10 $file_types.scoresEAF
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11 $file_types.varQuality
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12 #if $file_types.data_sources.data_source == "in"
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13 #for $v in $file_types.data_sources.varfiles <!--get each var file-->
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14 --Input_File ${v.input}
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15 #end for
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16 #else
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17 `cat $file_types.data_sources.varlist`
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18 #end if
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19
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20 #else if $file_types.file_type =="var1"
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21 List_Unique_Variants_2_1_0.pl --File_Type V --Output_File $output
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22 --Var_Type $file_types.variants
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23 $file_types.scores
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24 #if $file_types.data_sources.data_source == "in"
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25 #for $v in $file_types.data_sources.varfiles <!--get each var file-->
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26 --Input_File ${v.input}
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27 #end for
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28 #else
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29 `cat $file_types.data_sources.varlist`
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30 #end if
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31
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32 #else if $file_types.file_type =="gene"
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33 List_Unique_Variants_2_1_0.pl --File_Type G --Output_File $output
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34 --Var_Type $file_types.variants
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35 --Component $file_types.component
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36 --Impact $file_types.impact
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37 #if $file_types.data_sources.data_source == "in"
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38 #for $g in $file_types.data_sources.genefiles <!--get each var file-->
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39 --Input_File ${g.input}
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40 #end for
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41 #else
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42 `cat $file_types.data_sources.genelist`
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43 #end if
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44 #end if
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45 </command>
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46
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47 <outputs>
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48 <data format="tabular" name="output" />
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49 </outputs>
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50
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51 <inputs>
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52 <conditional name="file_types">
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53 <!--form field to select file type-->
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54 <param name="file_type" type="select" label="Select the input file type">
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55 <option value="var2" selected="True">var files, format 2.x</option>
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56 <option value="var1">var files, format 1.x</option>
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57 <option value="gene">gene files</option>
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58 </param>
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59
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60 <when value="var2">
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61 <!--form field to select all variant types to annotate-->
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62 <param name="variants" label="Select variant types to include" type="select" multiple="true" >
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63 <!--<validator type="no_options" message="Please select at least one variant type."/>-->
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64 <option value="All" selected="true">All</option>
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65 <option value="snp">snp</option>
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66 <option value="ins">ins</option>
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67 <option value="del">del</option>
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68 <option value="sub">sub</option>
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69 <option value="ref">ref</option>
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70 </param>
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71
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72 <!--form field to select varScoresVAF-->
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73 <param name="scoresVAF" type="select" label="Include varScoreVAF?">
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74 <option value="--Scores_VAF yes" selected="true">yes</option>
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75 <option value="--Scores_VAF no">no</option>
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76 </param>
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77 <!--form field to select varScoresEAF-->
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78 <param name="scoresEAF" type="select" label="Include varScoreEAF?">
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79 <option value="--Scores_EAF yes" selected="true">yes</option>
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80 <option value="--Scores_EAF no">no</option>
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81 </param>
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82 <!--form field to select varQuality-->
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83 <param name="varQuality" type="select" label="Include varQuality?">
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84 <option value="--Score_Qualities yes" selected="true">yes</option>
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85 <option value="--Score_Qualities no">no</option>
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86 </param>
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87
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88 <!--conditional to select variant file input-->
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89 <conditional name="data_sources">
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90 <param name="data_source" type="select" label="Where are the input var files?">
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91 <option value="in" selected="true">imported into Galaxy</option>
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92 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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93 </param>
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94 <when value="in">
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95 <!--form field to select variant files-->
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96 <repeat name="varfiles" title="Variant files">
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97 <param name="input" type="data" format="cg_var" label="Dataset">
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98 <validator type="unspecified_build" />
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99 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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100 metadata_name="dbkey" metadata_column="1"
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101 message="cgatools is not currently available for this build."/>
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102 </param>
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103 </repeat>
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104 </when>
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105 <when value="out">
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106 <!--form field to select crr file-->
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107 <param name="varlist" type="text" label="List of variant files (/path/file)" size="200" help="file with list of var files (/path/varfile), var files can be compressed (gz, bz2)."/>
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108 </when>
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109 </conditional>
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110 </when>
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111
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112 <when value="var1">
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113 <!--form field to select all variant types to annotate-->
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114 <param name="variants" label="Select variant types to include" type="select" multiple="true" >
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115 <!--<validator type="no_options" message="Please select at least one variant type."/>-->
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116 <option value="All" selected="true">All</option>
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117 <option value="snp">snp</option>
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118 <option value="ins">ins</option>
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119 <option value="del">del</option>
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120 <option value="sub">sub</option>
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121 <option value="ref">ref</option>
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122 </param>
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123
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124 <!--form field to select scores-->
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125 <param name="scores" type="select" label="Include totalScore?">
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126 <option value="--Scores yes" selected="true">yes</option>
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127 <option value="--Scores no">no</option>
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128 </param>
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129
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130 <!--conditional to select variant file input-->
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131 <conditional name="data_sources">
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132 <param name="data_source" type="select" label="Where are the input var files?">
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133 <option value="in" selected="true">imported into Galaxy</option>
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134 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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135 </param>
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136 <when value="in">
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137 <!--form field to select variant files-->
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138 <repeat name="varfiles" title="Variant files">
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139 <param name="input" type="data" format="cg_var" label="Dataset">
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140 <validator type="unspecified_build" />
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141 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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142 metadata_name="dbkey" metadata_column="1"
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143 message="cgatools is not currently available for this build."/>
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144 </param>
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145 </repeat>
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146 </when>
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147 <when value="out">
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148 <!--form field to select crr file-->
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149 <param name="varlist" type="text" label="List of variant files (/path/file)" size="200" help="file with list of var files (/path/varfile), var files can be compressed (gz, bz2)."/>
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150 </when>
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151 </conditional>
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152 </when>
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153
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154 <when value="gene">
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155 <!--form field to select all variant types to annotate-->
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156 <param name="variants" label="Select variant types to include" type="select" multiple="true" >
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157 <!--<validator type="no_options" message="Please select at least one variant type."/>-->
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158 <option value="All" selected="true">All</option>
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159 <option value="snp">snp</option>
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160 <option value="ins">ins</option>
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161 <option value="del">del</option>
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162 <option value="sub">sub</option>
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163 <option value="ref">ref</option>
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164 </param>
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165
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166 <!--form field to select component in gene file-->
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167 <param name="component" type="select" label="Select component types to include" multiple="true" >
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168 <option value="All" selected="true">All</option>
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169 <option value="CDS">CDS</option>
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170 <option value="INTRON">INTRON</option>
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171 <option value="DONOR">DONOR</option>
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172 <option value="ACCEPTOR">ACCEPTOR</option>
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173 <option value="TSS-UPSTREAM">TSS-UPSTREAM</option>
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174 <option value="SPAN5">SPAN5</option>
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175 <option value="SPAN3">SPAN3</option>
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176 <option value="SPAN">SPAN</option>
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177 <option value="UTR5">UTR5</option>
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178 <option value="UTR3">UTR3</option>
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179 <option value="UTR">UTR</option>
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180 </param>
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181
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182 <!--form field to select impact in gene file-->
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183 <param name="impact" type="select" label="Select impact types to include" multiple="true" >
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184 <option value="All" selected="true">All</option>
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185 <option value="NO-CHANGE">NO-CHANGE</option>
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186 <option value="SYNONYMOUS">SYNONYMOUS</option>
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187 <option value="MISSENES">MISSENES</option>
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188 <option value="NONSENSE">NONSENSE</option>
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189 <option value="NONSSTOP">NONSSTOP</option>
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190 <option value="DELETE">DELETE</option>
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191 <option value="INSERT">INSERT</option>
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192 <option value="DELETE+">DELETE+</option>
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193 <option value="INSERT+">INSERT+</option>
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194 <option value="FRAMESHIFT">FRAMESHIFT</option>
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195 <option value="MISSTART">MISSTART</option>
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196 <option value="DISRUPT">DISRUPT</option>
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197 <option value="UNKNOWN-VNC">UNKNOWN-VNC</option>
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198 <option value="UNKNOWN-INC">UNKNOWN-INC</option>
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199 <option value="UNKNOWN-TR">UNKNOWN-TR</option>
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200 </param>
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201
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202 <!--conditional to select gene file input-->
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203 <conditional name="data_sources">
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204 <param name="data_source" type="select" label="Where are the input gene files?">
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205 <option value="in" selected="true">imported into Galaxy</option>
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206 <option value="out">located outside Galaxy (available only for local Galaxy instances)</option>
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207 </param>
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208 <when value="in">
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209 <!--form field to select variant files-->
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210 <repeat name="genefiles" title="Gene files">
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211 <param name="input" type="data" format="cg_gene" label="Dataset">
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212 <validator type="unspecified_build" />
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213 <validator type="dataset_metadata_in_file" filename="cg_crr_files.loc"
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214 metadata_name="dbkey" metadata_column="1"
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215 message="cgatools is not currently available for this build."/>
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216 </param>
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217 </repeat>
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218 </when>
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219 <when value="out">
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220 <!--form field to select crr file-->
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221 <param name="genelist" type="text" label="List of gene files (/path/file)" size="200" help="file with list of gene files (/path/genefile), gene files can be compressed (gz, bz2)."/>
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222 </when>
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223 </conditional>
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224 </when>
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225
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226 </conditional>
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227 </inputs>
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228
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229
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230 <help>
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231
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232 **What it does**
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233
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234 This tool identifies all called variants present in the var or gene files and generates annotated variant list.
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235
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236 -----
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237
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238 **Instructions**::
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239
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240 List Unique Variants for Pipeline 1.x and 2.x
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241 [Uses header if available, checks for position of xref field if not]
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242 Take one or more var or gene files
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243 Extract a non-redundant set of variants
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244
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245 For var files:
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246 The fields used to define non-redundant variants are are:
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247 chromosome begin end varType reference alleleSeq xRef
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248 User can nominate class(es) of varType to filter on
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249 Outputs varScoreEAF, varScoreVAF and varQuality as a default but user can turn
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250 them off (separately)
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251 Scores and qualities stored in separate fields, all values for a variant across
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252 a set of genomes.
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253 Values for different genomes separated by ':', for two hom entries for the same
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254 genome by '|'
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255 Output is accepted by testvariants to generate a variant table, all fields kept
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256 in testvariants output
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257
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258 For gene files:
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259 The fields used to define non-redundant gene variants are:
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260 chromosome begin end varType reference call xRef geneId mrnaAcc proteinAcc symbol
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261 orientation component componentIndex codingRegionKnown impact nucleotidePos
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262 proteinPos annotationRefSequence sampleSequence genomeRefSequence
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263 User can nominate class(es) of varType, component or impact to filter on
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264 All gene entries kept ie multiple entries if multiple transcripts
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265
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266 NB Now treating xref as a separate component in var recs, as it is not consistent
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267 between X and Y vars
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268 Not fixed for gene recs yet
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269
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270 perl List_Unique_Variants_2_0_11.pl
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271 --File_Type [V|G]
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272 --Input_File input_file_1 [set of var or gene files]
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273 --Input_File input_file_2
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274 ...
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275 --Input_File input_file_n
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276 --Output_File filename
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277 --Var_Type [For both file types, 'All' or any value from the varType field,
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278 multiple values allowed, separated by comma]
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279 --Component [Gene file specific,'All' or any value from component field of gene
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280 file, multiple allowed; 'All" is default]
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281 --Impact All [Gene file specific,'All' or any value from impact field of gene
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282 file, multiple allowed; 'All" is default]
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283 --Scores [1.x var file specific, yes|no, yes is default]
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284 --Scores_VAF [2.0 var file specific, yes|no, yes is default]
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285 --Scores_EAF [2.0 var file specific, yes|no, yes is default]
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286 --Score_Qualities [yes|no, yes is default]
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287 eg
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288 perl List_Unique_Variants_2_0_11.pl \
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289 --File_Type V \
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290 --Input_File /Yoruban_Trio_1100_37/GS19238-1100-37/GS00028-DNA_A01/ASM/gene-GS19238-1100-37-ASM.tsv.bz2 \
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291 --Input_File /Yoruban_Trio_1100_37/GS19239-1100-37/GS00028-DNA_B01/ASM/gene-GS19239-1100-37-ASM.tsv.bz2 \
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292 --Input_File /Yoruban_Trio_1100_37/GS19240-1100-37/GS00028-DNA_C01/ASM/gene-GS19240-1100-37-ASM.tsv.bz2 \
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293 --Output_File /Users/rtearle/Documents/TBF/YRI_Trio_Protein_Coding.tsv \
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294 --Var_Type All
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295 --Component All
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296 --Impact All
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297 --Scores_VAF yes \
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298 --Scores_EAF yes \
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299 --Score_Qualities yes
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300
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301 var fields
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302 1.x locus ploidy haplotype chromosome begin end varType reference alleleSeq
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303 totalScore hapLink xRef
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304 2.0 locus ploidy allele chromosome begin end varType reference alleleSeq
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305 varScoreVAF varScoreEAF varQuality hapLink xRef
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306
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307 gene fields
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308 1.x index locus allele chromosome begin end varType reference call xRef geneId
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309 mrnaAcc proteinAcc symbol orientation component componentIndex
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310 codingRegionKnown impact nucleotidePos proteinPos annotationRefSequence
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311 sampleSequence genomeRefSequence
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312 2.0 index locus allele chromosome begin end varType reference call xRef geneId
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313 mrnaAcc proteinAcc symbol orientation component componentIndex hasCodingRegion
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314 impact nucleotidePos proteinPos annotationRefSequence sampleSequence
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315 genomeRefSequence pfam
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316
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317 Parsing and storing input parameters
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318 Only input_file fields can be repeated
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319 input paramaters are case insensitive
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320
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321
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322 </help>
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323 </tool>
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