root/galaxy-central/tools/metag_tools/mapping_to_ucsc.xml @ 2

リビジョン 2, 8.4 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central
行番号 
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
148This 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
156This tool requires the mapping data to contain at least the following information:
157
158chromosome, 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
164For 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
177running 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>
Note: リポジトリブラウザについてのヘルプは TracBrowser を参照してください。