Mercurial > repos > devteam > mapping_to_ucsc
annotate mapping_to_ucsc.xml @ 1:7293ec9e0afc draft default tip
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:25:02 -0400 |
| parents | cf8d47e49c21 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <tool id="mapToUCSC" name="Format mapping data" version="1.0.0"> |
| 2 <description> as UCSC custom track</description> | |
| 3 <command interpreter="python"> | |
| 4 mapping_to_ucsc.py | |
| 5 $out_file1 | |
| 6 $input | |
| 7 $chr_col | |
| 8 $coord_col | |
| 9 $track.track_type | |
| 10 #if $track.track_type == "coverage" or $track.track_type == "both" | |
| 11 $track.coverage_col | |
| 12 "${track.cname}" | |
| 13 "${track.cdescription}" | |
| 14 "${track.ccolor}" | |
| 15 "${track.cvisibility}" | |
| 16 #end if | |
| 17 #if $track.track_type == "snp" or $track.track_type == "both" | |
| 18 "${track.sdescription}" | |
| 19 "${track.svisibility}" | |
| 20 $track.col2 | |
| 21 #end if | |
| 22 </command> | |
| 23 <inputs> | |
| 24 <param format="tabular" name="input" type="data" label="Select mapping data"/> | |
| 25 <param name="chr_col" type="data_column" data_ref="input" label="Column for reference chromosome" /> | |
| 26 <param name="coord_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for reference co-ordinate" /> | |
| 27 <conditional name="track"> | |
| 28 <param name="track_type" type="select" label="Display"> | |
| 29 <option value="snp" selected="true">SNPs</option> | |
| 30 <option value="coverage">Read coverage</option> | |
| 31 <option value="both">Both</option> | |
| 32 </param> | |
| 33 <when value = "coverage"> | |
| 34 <param name="coverage_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for read coverage" /> | |
|
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7293ec9e0afc
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
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changeset
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35 <param name="cname" type="text" value="User Track" label="Coverage track name"> |
| 0 | 36 <validator type="length" max="15"/> |
| 37 </param> | |
| 38 <param name="cdescription" type="text" value="User Supplied Coverage Track (from Galaxy)" label="Coverage track description"> | |
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7293ec9e0afc
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
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changeset
|
39 <validator type="length" max="60"/> |
| 0 | 40 </param> |
| 41 <param label="Coverage track Color" name="ccolor" type="select"> | |
| 42 <option selected="yes" value="0-0-0">Black</option> | |
| 43 <option value="255-0-0">Red</option> | |
| 44 <option value="0-255-0">Green</option> | |
| 45 <option value="0-0-255">Blue</option> | |
| 46 <option value="255-0-255">Magenta</option> | |
| 47 <option value="0-255-255">Cyan</option> | |
| 48 <option value="255-215-0">Gold</option> | |
| 49 <option value="160-32-240">Purple</option> | |
| 50 <option value="255-140-0">Orange</option> | |
| 51 <option value="255-20-147">Pink</option> | |
| 52 <option value="92-51-23">Dark Chocolate</option> | |
| 53 <option value="85-107-47">Olive green</option> | |
| 54 </param> | |
| 55 <param label="Coverage track Visibility" name="cvisibility" type="select"> | |
| 56 <option selected="yes" value="1">Dense</option> | |
| 57 <option value="2">Full</option> | |
| 58 <option value="3">Pack</option> | |
| 59 <option value="4">Squish</option> | |
| 60 <option value="0">Hide</option> | |
| 61 </param> | |
| 62 </when> | |
| 63 | |
| 64 <when value = "snp"> | |
| 65 <!-- | |
| 66 <param name="col1" type="data_column" data_ref="input" label="Column containing the reference nucleotide" /> | |
| 67 --> | |
| 68 <param name="col2" type="data_column" data_ref="input" label="Column containing the read nucleotide" /> | |
| 69 <!-- | |
|
1
7293ec9e0afc
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
70 <param name="sname" type="text" value="User Track-2" label="SNP track name"> |
| 0 | 71 <validator type="length" max="15"/> |
| 72 </param> | |
| 73 --> | |
| 74 <param name="sdescription" type="text" value="User Supplied Track (from Galaxy)" label="SNP track description"> | |
|
1
7293ec9e0afc
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
75 <validator type="length" max="60"/> |
| 0 | 76 </param> |
| 77 <param label="SNP track Visibility" name="svisibility" type="select"> | |
| 78 <option selected="yes" value="1">Dense</option> | |
| 79 <option value="2">Full</option> | |
| 80 <option value="3">Pack</option> | |
| 81 <option value="4">Squish</option> | |
| 82 <option value="0">Hide</option> | |
| 83 </param> | |
| 84 </when> | |
| 85 | |
| 86 <when value = "both"> | |
| 87 <param name="coverage_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for read coverage" /> | |
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1
7293ec9e0afc
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
88 <param name="cname" type="text" value="User Track" label="Coverage track name"> |
| 0 | 89 <validator type="length" max="15"/> |
| 90 </param> | |
|
1
7293ec9e0afc
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
91 <param name="cdescription" type="text" value="User Supplied Track (from Galaxy)" label="Coverage track description"> |
| 0 | 92 <validator type="length" max="60"/> |
| 93 </param> | |
| 94 <param label="Coverage track Color" name="ccolor" type="select"> | |
| 95 <option selected="yes" value="0-0-0">Black</option> | |
| 96 <option value="255-0-0">Red</option> | |
| 97 <option value="0-255-0">Green</option> | |
| 98 <option value="0-0-255">Blue</option> | |
| 99 <option value="255-0-255">Magenta</option> | |
| 100 <option value="0-255-255">Cyan</option> | |
| 101 <option value="255-215-0">Gold</option> | |
| 102 <option value="160-32-240">Purple</option> | |
| 103 <option value="255-140-0">Orange</option> | |
| 104 <option value="255-20-147">Pink</option> | |
| 105 <option value="92-51-23">Dark Chocolate</option> | |
| 106 <option value="85-107-47">Olive green</option> | |
| 107 </param> | |
| 108 <param label="Coverage track Visibility" name="cvisibility" type="select"> | |
| 109 <option selected="yes" value="1">Dense</option> | |
| 110 <option value="2">Full</option> | |
| 111 <option value="3">Pack</option> | |
| 112 <option value="4">Squish</option> | |
| 113 <option value="0">Hide</option> | |
| 114 </param> | |
| 115 <!-- | |
| 116 <param name="col1" type="data_column" data_ref="input" label="Column containing the reference nucleotide" /> | |
| 117 --> | |
| 118 <param name="col2" type="data_column" data_ref="input" label="Column containing the read nucleotide" /> | |
| 119 <!-- | |
|
1
7293ec9e0afc
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
120 <param name="sname" type="text" value="User Track-2" label="SNP track name"> |
| 0 | 121 <validator type="length" max="15"/> |
| 122 </param> | |
| 123 --> | |
|
1
7293ec9e0afc
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
devteam
parents:
0
diff
changeset
|
124 <param name="sdescription" type="text" value="User Supplied Track (from Galaxy)" label="SNP track description"> |
| 0 | 125 <validator type="length" max="60"/> |
| 126 </param> | |
| 127 <param label="SNP track Visibility" name="svisibility" type="select"> | |
| 128 <option selected="yes" value="1">Dense</option> | |
| 129 <option value="2">Full</option> | |
| 130 <option value="3">Pack</option> | |
| 131 <option value="4">Squish</option> | |
| 132 <option value="0">Hide</option> | |
| 133 </param> | |
| 134 </when> | |
| 135 </conditional> | |
| 136 </inputs> | |
| 137 <outputs> | |
| 138 <data format="customtrack" name="out_file1"/> | |
| 139 </outputs> | |
| 140 | |
| 141 | |
| 142 <help> | |
| 143 | |
| 144 .. class:: infomark | |
| 145 | |
| 146 **What it does** | |
| 147 | |
| 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. | |
| 149 | |
| 150 ----- | |
| 151 | |
| 152 .. class:: warningmark | |
| 153 | |
| 154 **Note** | |
| 155 | |
| 156 This tool requires the mapping data to contain at least the following information: | |
| 157 | |
| 158 chromosome, genome coordinate, read nucleotide (if option to display is SNPs), read coverage (if option to display is Read coverage). | |
| 159 | |
| 160 ----- | |
| 161 | |
| 162 **Example** | |
| 163 | |
| 164 For the following Mapping data:: | |
| 165 | |
| 166 #chr g_start read_id read_coord g_nt read_nt qual read_coverage | |
| 167 chrM 1 1:29:1672:1127/1 11 G G 40 134 | |
| 168 chrM 1 1:32:93:933/1 4 G A 40 134 | |
| 169 chrM 1 1:34:116:2032/1 11 G A 40 134 | |
| 170 chrM 1 1:39:207:964/1 1 G G 40 134 | |
| 171 chrM 2 1:3:359:848/1 1 G C 40 234 | |
| 172 chrM 2 1:40:1435:1013/1 1 G G 40 234 | |
| 173 chrM 3 1:40:730:972/1 9 G G 40 334 | |
| 174 chrM 4 1:42:1712:921/2 31 G T 35 434 | |
| 175 chrM 4 1:44:1649:493/1 4 G G 40 434 | |
| 176 | |
| 177 running this tool to display both SNPs and Read coverage will return the following tracks, containing aggregated data per genome co-ordinate:: | |
| 178 | |
| 179 track type=wiggle_0 name="Coverage Track" description="User Supplied Track (from Galaxy)" color=0,0,0 visibility=1 | |
| 180 variableStep chrom=chrM | |
| 181 1 134 | |
| 182 2 234 | |
| 183 3 334 | |
| 184 4 434 | |
| 185 track type=wiggle_0 name="Track A" description="User Supplied SNP Track (from Galaxy)" color=255,0,0 visibility=1 | |
| 186 variableStep chrom=chrM | |
| 187 1 2 | |
| 188 track type=wiggle_0 name="Track T" description="User Supplied SNP Track (from Galaxy)" color=0,255,0 visibility=1 | |
| 189 variableStep chrom=chrM | |
| 190 4 1 | |
| 191 track type=wiggle_0 name="Track G" description="User Supplied SNP Track (from Galaxy)" color=0,0,255 visibility=1 | |
| 192 variableStep chrom=chrM | |
| 193 1 2 | |
| 194 2 1 | |
| 195 3 1 | |
| 196 4 1 | |
| 197 track type=wiggle_0 name="Track C" description="User Supplied SNP Track (from Galaxy)" color=255,0,255 visibility=1 | |
| 198 variableStep chrom=chrM | |
| 199 2 1 | |
| 200 | |
| 201 </help> | |
| 202 </tool> |