[2] | 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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