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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