annotate mapping_to_ucsc.xml @ 0:601abbd22cea draft

Imported from capsule None
author devteam
date Mon, 19 May 2014 12:33:55 -0400
parents
children 5385aceef9e9
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
1 <tool id="mapToUCSC" name="Format mapping data" version="1.0.0">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
2 <description> as UCSC custom track</description>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
3 <command interpreter="python">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
4 mapping_to_ucsc.py
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
5 $out_file1
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
6 $input
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
7 $chr_col
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
8 $coord_col
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
9 $track.track_type
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
10 #if $track.track_type == "coverage" or $track.track_type == "both"
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
11 $track.coverage_col
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
12 "${track.cname}"
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
13 "${track.cdescription}"
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
14 "${track.ccolor}"
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
15 "${track.cvisibility}"
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
16 #end if
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
17 #if $track.track_type == "snp" or $track.track_type == "both"
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
18 "${track.sdescription}"
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
19 "${track.svisibility}"
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
20 $track.col2
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
21 #end if
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
22 </command>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
23 <inputs>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
24 <param format="tabular" name="input" type="data" label="Select mapping data"/>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
25 <param name="chr_col" type="data_column" data_ref="input" label="Column for reference chromosome" />
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
26 <param name="coord_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for reference co-ordinate" />
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
27 <conditional name="track">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
28 <param name="track_type" type="select" label="Display">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
29 <option value="snp" selected="true">SNPs</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
30 <option value="coverage">Read coverage</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
31 <option value="both">Both</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
32 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
33 <when value = "coverage">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
34 <param name="coverage_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for read coverage" />
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
35 <param name="cname" type="text" size="15" value="User Track" label="Coverage track name">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
36 <validator type="length" max="15"/>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
37 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
38 <param name="cdescription" type="text" value="User Supplied Coverage Track (from Galaxy)" label="Coverage track description">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
39 <validator type="length" max="60" size="15"/>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
40 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
41 <param label="Coverage track Color" name="ccolor" type="select">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
42 <option selected="yes" value="0-0-0">Black</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
43 <option value="255-0-0">Red</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
44 <option value="0-255-0">Green</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
45 <option value="0-0-255">Blue</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
46 <option value="255-0-255">Magenta</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
47 <option value="0-255-255">Cyan</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
48 <option value="255-215-0">Gold</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
49 <option value="160-32-240">Purple</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
50 <option value="255-140-0">Orange</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
51 <option value="255-20-147">Pink</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
52 <option value="92-51-23">Dark Chocolate</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
53 <option value="85-107-47">Olive green</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
54 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
55 <param label="Coverage track Visibility" name="cvisibility" type="select">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
56 <option selected="yes" value="1">Dense</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
57 <option value="2">Full</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
58 <option value="3">Pack</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
59 <option value="4">Squish</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
60 <option value="0">Hide</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
61 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
62 </when>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
63
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
64 <when value = "snp">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
65 <!--
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
66 <param name="col1" type="data_column" data_ref="input" label="Column containing the reference nucleotide" />
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
67 -->
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
68 <param name="col2" type="data_column" data_ref="input" label="Column containing the read nucleotide" />
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
69 <!--
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
70 <param name="sname" type="text" size="15" value="User Track-2" label="SNP track name">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
71 <validator type="length" max="15"/>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
72 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
73 -->
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
74 <param name="sdescription" type="text" value="User Supplied Track (from Galaxy)" label="SNP track description">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
75 <validator type="length" max="60" size="15"/>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
76 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
77 <param label="SNP track Visibility" name="svisibility" type="select">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
78 <option selected="yes" value="1">Dense</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
79 <option value="2">Full</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
80 <option value="3">Pack</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
81 <option value="4">Squish</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
82 <option value="0">Hide</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
83 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
84 </when>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
85
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
86 <when value = "both">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
87 <param name="coverage_col" type="data_column" data_ref="input" numerical="True" label="Numerical column for read coverage" />
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
88 <param name="cname" type="text" size="15" value="User Track" label="Coverage track name">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
89 <validator type="length" max="15"/>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
90 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
91 <param name="cdescription" type="text" size="15" value="User Supplied Track (from Galaxy)" label="Coverage track description">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
92 <validator type="length" max="60"/>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
93 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
94 <param label="Coverage track Color" name="ccolor" type="select">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
95 <option selected="yes" value="0-0-0">Black</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
96 <option value="255-0-0">Red</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
97 <option value="0-255-0">Green</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
98 <option value="0-0-255">Blue</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
99 <option value="255-0-255">Magenta</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
100 <option value="0-255-255">Cyan</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
101 <option value="255-215-0">Gold</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
102 <option value="160-32-240">Purple</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
103 <option value="255-140-0">Orange</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
104 <option value="255-20-147">Pink</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
105 <option value="92-51-23">Dark Chocolate</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
106 <option value="85-107-47">Olive green</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
107 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
108 <param label="Coverage track Visibility" name="cvisibility" type="select">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
109 <option selected="yes" value="1">Dense</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
110 <option value="2">Full</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
111 <option value="3">Pack</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
112 <option value="4">Squish</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
113 <option value="0">Hide</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
114 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
115 <!--
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
116 <param name="col1" type="data_column" data_ref="input" label="Column containing the reference nucleotide" />
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
117 -->
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
118 <param name="col2" type="data_column" data_ref="input" label="Column containing the read nucleotide" />
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
119 <!--
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
120 <param name="sname" type="text" size="15" value="User Track-2" label="SNP track name">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
121 <validator type="length" max="15"/>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
122 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
123 -->
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
124 <param name="sdescription" type="text" size="15" value="User Supplied Track (from Galaxy)" label="SNP track description">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
125 <validator type="length" max="60"/>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
126 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
127 <param label="SNP track Visibility" name="svisibility" type="select">
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
128 <option selected="yes" value="1">Dense</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
129 <option value="2">Full</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
130 <option value="3">Pack</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
131 <option value="4">Squish</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
132 <option value="0">Hide</option>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
133 </param>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
134 </when>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
135 </conditional>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
136 </inputs>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
137 <outputs>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
138 <data format="customtrack" name="out_file1"/>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
139 </outputs>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
140
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
141
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
142 <help>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
143
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
144 .. class:: infomark
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
145
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
146 **What it does**
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
147
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
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.
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
149
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
150 -----
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
151
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
152 .. class:: warningmark
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
153
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
154 **Note**
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
155
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
156 This tool requires the mapping data to contain at least the following information:
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
157
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
158 chromosome, genome coordinate, read nucleotide (if option to display is SNPs), read coverage (if option to display is Read coverage).
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
159
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
160 -----
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
161
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
162 **Example**
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
163
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
164 For the following Mapping data::
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
165
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
166 #chr g_start read_id read_coord g_nt read_nt qual read_coverage
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
167 chrM 1 1:29:1672:1127/1 11 G G 40 134
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
168 chrM 1 1:32:93:933/1 4 G A 40 134
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
169 chrM 1 1:34:116:2032/1 11 G A 40 134
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
170 chrM 1 1:39:207:964/1 1 G G 40 134
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
171 chrM 2 1:3:359:848/1 1 G C 40 234
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
172 chrM 2 1:40:1435:1013/1 1 G G 40 234
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
173 chrM 3 1:40:730:972/1 9 G G 40 334
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
174 chrM 4 1:42:1712:921/2 31 G T 35 434
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
175 chrM 4 1:44:1649:493/1 4 G G 40 434
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
176
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
177 running this tool to display both SNPs and Read coverage will return the following tracks, containing aggregated data per genome co-ordinate::
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
178
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
179 track type=wiggle_0 name="Coverage Track" description="User Supplied Track (from Galaxy)" color=0,0,0 visibility=1
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
180 variableStep chrom=chrM
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
181 1 134
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
182 2 234
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
183 3 334
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
184 4 434
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
185 track type=wiggle_0 name="Track A" description="User Supplied SNP Track (from Galaxy)" color=255,0,0 visibility=1
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
186 variableStep chrom=chrM
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
187 1 2
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
188 track type=wiggle_0 name="Track T" description="User Supplied SNP Track (from Galaxy)" color=0,255,0 visibility=1
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
189 variableStep chrom=chrM
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
190 4 1
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
191 track type=wiggle_0 name="Track G" description="User Supplied SNP Track (from Galaxy)" color=0,0,255 visibility=1
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
192 variableStep chrom=chrM
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
193 1 2
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
194 2 1
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
195 3 1
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
196 4 1
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
197 track type=wiggle_0 name="Track C" description="User Supplied SNP Track (from Galaxy)" color=255,0,255 visibility=1
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
198 variableStep chrom=chrM
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
199 2 1
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
200
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
201 </help>
601abbd22cea Imported from capsule None
devteam
parents:
diff changeset
202 </tool>