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1 <tool id="mapToUCSC" name="Format mapping data" version="1.0.0">
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2 <description> as UCSC custom track</description>
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3 <command interpreter="python">
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4 mapping_to_ucsc.py
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5 $out_file1
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6 $input
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7 $chr_col
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8 $coord_col
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9 $track.track_type
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10 #if $track.track_type == "coverage" or $track.track_type == "both"
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11 $track.coverage_col
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12 "${track.cname}"
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13 "${track.cdescription}"
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14 "${track.ccolor}"
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15 "${track.cvisibility}"
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16 #end if
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17 #if $track.track_type == "snp" or $track.track_type == "both"
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18 "${track.sdescription}"
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19 "${track.svisibility}"
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20 $track.col2
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21 #end if
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22 </command>
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23 <inputs>
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24 <param format="tabular" name="input" type="data" label="Select mapping data"/>
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25 <param name="chr_col" type="data_column" data_ref="input" label="Column for reference chromosome" />
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26 <param name="coord_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for reference co-ordinate" />
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27 <conditional name="track">
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28 <param name="track_type" type="select" label="Display">
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29 <option value="snp" selected="true">SNPs</option>
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30 <option value="coverage">Read coverage</option>
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31 <option value="both">Both</option>
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32 </param>
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33 <when value = "coverage">
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34 <param name="coverage_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for read coverage" />
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35 <param name="cname" type="text" size="15" value="User Track" label="Coverage track name">
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36 <validator type="length" max="15"/>
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37 </param>
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38 <param name="cdescription" type="text" value="User Supplied Coverage Track (from Galaxy)" label="Coverage track description">
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39 <validator type="length" max="60" size="15"/>
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40 </param>
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41 <param label="Coverage track Color" name="ccolor" type="select">
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42 <option selected="yes" value="0-0-0">Black</option>
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43 <option value="255-0-0">Red</option>
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44 <option value="0-255-0">Green</option>
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45 <option value="0-0-255">Blue</option>
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46 <option value="255-0-255">Magenta</option>
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47 <option value="0-255-255">Cyan</option>
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48 <option value="255-215-0">Gold</option>
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49 <option value="160-32-240">Purple</option>
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50 <option value="255-140-0">Orange</option>
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51 <option value="255-20-147">Pink</option>
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52 <option value="92-51-23">Dark Chocolate</option>
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53 <option value="85-107-47">Olive green</option>
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54 </param>
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55 <param label="Coverage track Visibility" name="cvisibility" type="select">
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56 <option selected="yes" value="1">Dense</option>
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57 <option value="2">Full</option>
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58 <option value="3">Pack</option>
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59 <option value="4">Squish</option>
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60 <option value="0">Hide</option>
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61 </param>
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62 </when>
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63
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64 <when value = "snp">
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65 <!--
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66 <param name="col1" type="data_column" data_ref="input" label="Column containing the reference nucleotide" />
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67 -->
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68 <param name="col2" type="data_column" data_ref="input" label="Column containing the read nucleotide" />
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69 <!--
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70 <param name="sname" type="text" size="15" value="User Track-2" label="SNP track name">
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71 <validator type="length" max="15"/>
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72 </param>
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73 -->
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74 <param name="sdescription" type="text" value="User Supplied Track (from Galaxy)" label="SNP track description">
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75 <validator type="length" max="60" size="15"/>
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76 </param>
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77 <param label="SNP track Visibility" name="svisibility" type="select">
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78 <option selected="yes" value="1">Dense</option>
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79 <option value="2">Full</option>
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80 <option value="3">Pack</option>
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81 <option value="4">Squish</option>
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82 <option value="0">Hide</option>
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83 </param>
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84 </when>
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85
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86 <when value = "both">
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87 <param name="coverage_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for read coverage" />
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88 <param name="cname" type="text" size="15" value="User Track" label="Coverage track name">
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89 <validator type="length" max="15"/>
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90 </param>
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91 <param name="cdescription" type="text" size="15" value="User Supplied Track (from Galaxy)" label="Coverage track description">
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92 <validator type="length" max="60"/>
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93 </param>
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94 <param label="Coverage track Color" name="ccolor" type="select">
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95 <option selected="yes" value="0-0-0">Black</option>
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96 <option value="255-0-0">Red</option>
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97 <option value="0-255-0">Green</option>
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98 <option value="0-0-255">Blue</option>
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99 <option value="255-0-255">Magenta</option>
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100 <option value="0-255-255">Cyan</option>
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101 <option value="255-215-0">Gold</option>
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102 <option value="160-32-240">Purple</option>
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103 <option value="255-140-0">Orange</option>
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104 <option value="255-20-147">Pink</option>
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105 <option value="92-51-23">Dark Chocolate</option>
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106 <option value="85-107-47">Olive green</option>
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107 </param>
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108 <param label="Coverage track Visibility" name="cvisibility" type="select">
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109 <option selected="yes" value="1">Dense</option>
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110 <option value="2">Full</option>
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111 <option value="3">Pack</option>
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112 <option value="4">Squish</option>
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113 <option value="0">Hide</option>
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114 </param>
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115 <!--
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116 <param name="col1" type="data_column" data_ref="input" label="Column containing the reference nucleotide" />
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117 -->
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118 <param name="col2" type="data_column" data_ref="input" label="Column containing the read nucleotide" />
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119 <!--
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120 <param name="sname" type="text" size="15" value="User Track-2" label="SNP track name">
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121 <validator type="length" max="15"/>
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122 </param>
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123 -->
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124 <param name="sdescription" type="text" size="15" value="User Supplied Track (from Galaxy)" label="SNP track description">
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125 <validator type="length" max="60"/>
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126 </param>
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127 <param label="SNP track Visibility" name="svisibility" type="select">
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128 <option selected="yes" value="1">Dense</option>
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129 <option value="2">Full</option>
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130 <option value="3">Pack</option>
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131 <option value="4">Squish</option>
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132 <option value="0">Hide</option>
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133 </param>
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134 </when>
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135 </conditional>
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136 </inputs>
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137 <outputs>
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138 <data format="customtrack" name="out_file1"/>
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139 </outputs>
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140
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141
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142 <help>
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143
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144 .. class:: infomark
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145
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146 **What it does**
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147
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148 This tool turns mapping data generated by short read mappers into a format that can be displayed in the UCSC genome browser as a custom track.
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149
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150 -----
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151
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152 .. class:: warningmark
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153
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154 **Note**
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155
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156 This tool requires the mapping data to contain at least the following information:
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157
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158 chromosome, genome coordinate, read nucleotide (if option to display is SNPs), read coverage (if option to display is Read coverage).
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159
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160 -----
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161
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162 **Example**
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163
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164 For the following Mapping data::
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165
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166 #chr g_start read_id read_coord g_nt read_nt qual read_coverage
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167 chrM 1 1:29:1672:1127/1 11 G G 40 134
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168 chrM 1 1:32:93:933/1 4 G A 40 134
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169 chrM 1 1:34:116:2032/1 11 G A 40 134
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170 chrM 1 1:39:207:964/1 1 G G 40 134
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171 chrM 2 1:3:359:848/1 1 G C 40 234
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172 chrM 2 1:40:1435:1013/1 1 G G 40 234
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173 chrM 3 1:40:730:972/1 9 G G 40 334
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174 chrM 4 1:42:1712:921/2 31 G T 35 434
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175 chrM 4 1:44:1649:493/1 4 G G 40 434
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176
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177 running this tool to display both SNPs and Read coverage will return the following tracks, containing aggregated data per genome co-ordinate::
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178
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179 track type=wiggle_0 name="Coverage Track" description="User Supplied Track (from Galaxy)" color=0,0,0 visibility=1
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180 variableStep chrom=chrM
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181 1 134
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182 2 234
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183 3 334
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184 4 434
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185 track type=wiggle_0 name="Track A" description="User Supplied SNP Track (from Galaxy)" color=255,0,0 visibility=1
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186 variableStep chrom=chrM
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187 1 2
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188 track type=wiggle_0 name="Track T" description="User Supplied SNP Track (from Galaxy)" color=0,255,0 visibility=1
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189 variableStep chrom=chrM
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190 4 1
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191 track type=wiggle_0 name="Track G" description="User Supplied SNP Track (from Galaxy)" color=0,0,255 visibility=1
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192 variableStep chrom=chrM
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193 1 2
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194 2 1
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195 3 1
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196 4 1
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197 track type=wiggle_0 name="Track C" description="User Supplied SNP Track (from Galaxy)" color=255,0,255 visibility=1
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198 variableStep chrom=chrM
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199 2 1
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200
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201 </help>
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202 </tool>
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