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comparison mapping_to_ucsc.xml @ 0:601abbd22cea draft

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Imported from capsule None
author devteam
date Mon, 19 May 2014 12:33:55 -0400
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children 5385aceef9e9
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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" />
35 <param name="cname" type="text" size="15" value="User Track" label="Coverage track name">
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">
39 <validator type="length" max="60" size="15"/>
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 <!--
70 <param name="sname" type="text" size="15" value="User Track-2" label="SNP track name">
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">
75 <validator type="length" max="60" size="15"/>
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" />
88 <param name="cname" type="text" size="15" value="User Track" label="Coverage track name">
89 <validator type="length" max="15"/>
90 </param>
91 <param name="cdescription" type="text" size="15" value="User Supplied Track (from Galaxy)" label="Coverage track description">
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 <!--
120 <param name="sname" type="text" size="15" value="User Track-2" label="SNP track name">
121 <validator type="length" max="15"/>
122 </param>
123 -->
124 <param name="sdescription" type="text" size="15" value="User Supplied Track (from Galaxy)" label="SNP track description">
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>