annotate synteny-mapper.xml @ 25:1fdfbe87a959 draft default tip

Uploaded
author s-kaufmann
date Tue, 19 Aug 2014 08:18:03 -0400
parents 8a4190457eb7
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
1 <tool id="SyntenyMapper1" name="SyntenyMapper" version="1.0.0">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
2 <description>Maps maximum stretches of orthologous genes with conserved order within large synteny regions</description>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
3
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
4 <requirements>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
5 <requirement type="set_environment">JAR_PATH</requirement>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
6 </requirements>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
7
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
8 <command>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
9 #if $source.source_select == "ensembl" #java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/mapping/SyntenyMapper $source.ensembl_version $inputSyntenyRegions $inputHomologousGenes $out_file1 $out_file2 $source.species.species1 $source.species.species2 $source.filter
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
10 #else #java -cp \$JAR_PATH/syntenyMapper.jar de/tum/wzw/mapping/SyntenyMapper $inputSyntenyRegions $inputHomologousGenes $out_file1 $out_file2 $source.species1 $source.species2
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
11 #end if
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
12
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
13 </command>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
14
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
15 <inputs>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
16
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
17
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
18
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
19 <conditional name="source">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
20 <param name="source_select" type="select" label="Data source">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
21 <option value="ensembl">ENSEMBL download</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
22 <option value="upload">Own data upload</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
23 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
24 <when value="ensembl">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
25 <param name="ensembl_version" type="integer" value="73" label="ENSEMBL Compara version"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
26 <conditional name="species">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
27 <param name="species1" type="select" label="Species1">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
28 <option value="felis_catus">Felis catus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
29 <option value="rattus_norvegicus">Rattus norvegicus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
30 <option value="meleagris_gallopavo">Meleagris gallopavo</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
31 <option value="monodelphis_domestica">Monodelphis domestica</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
32 <option value="mus_musculus">Mus musculus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
33 <option value="canis_familiaris">Canis familiaris</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
34 <option value="oryctolagus_cuniculus">Oryctolagus cuniculus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
35 <option value="equus_caballus">Equus caballus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
36 <option value="gallus_gallus">Gallus gallus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
37 <option value="macaca_mulatta">Macaca mulatta</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
38 <option value="pongo_abelii">Pongo abelii</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
39 <option value="sus_scrofa">Sus scrofa</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
40 <option value="gorilla_gorilla">Gorilla gorilla</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
41 <option value="callithrix_jacchus">Callithrix jacchus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
42 <option value="ornithorhynchus_anatinus">Ornithorhynchus anatinus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
43 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
44 <option value="anolis_carolinensis">Anolis carolinensis</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
45 <option value="pan_troglodytes">Pan troglodytes</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
46 <option value="bos_taurus">Bos taurus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
47 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
48 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
49 <when value="felis_catus">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
50 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
51 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
52 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
53 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
54 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
55 <when value="rattus_norvegicus">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
56 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
57 <option value="mus_musculus">Mus musculus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
58 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
59 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
60 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
61 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
62 <when value="meleagris_gallopavo">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
63 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
64 <option value="gallus_gallus">Gallus gallus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
65 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
66 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
67 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
68 <when value="monodelphis_domestica">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
69 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
70 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
71 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
72 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
73 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
74 <when value="mus_musculus">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
75 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
76 <option value="sus_scrofa">Sus scrofa</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
77 <option value="rattus_norvegicus">Rattus norvegicus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
78 <option value="ornithorhynchus_anatinus">Ornithorhynchus anatinus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
79 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
80 <option value="canis_familiaris">Canis familiaris</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
81 <option value="gallus_gallus">Gallus gallus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
82 <option value="bos_taurus">Bos taurus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
83 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
84 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
85 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
86 <when value="canis_familiaris">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
87 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
88 <option value="mus_musculus">Mus musculus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
89 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
90 <option value="equus_caballus">Equus caballus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
91 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
92 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
93 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
94 <when value="oryctolagus_cuniculus">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
95 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
96 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
97 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
98 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
99 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
100 <when value="equus_caballus">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
101 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
102 <option value="canis_familiaris">Canis familiaris</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
103 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
104 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
105 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
106 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
107 <when value="gallus_gallus">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
108 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
109 <option value="meleagris_gallopavo">Meleagris gallopavo</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
110 <option value="mus_musculus">Mus musculus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
111 <option value="anolis_carolinensis">Anolis carolinensis</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
112 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
113 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
114 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
115 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
116 <when value="macaca_mulatta">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
117 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
118 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
119 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
120 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
121 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
122 <when value="pongo_abelii">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
123 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
124 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
125 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
126 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
127 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
128 <when value="sus_scrofa">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
129 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
130 <option value="mus_musculus">Mus musculus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
131 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
132 <option value="bos_taurus">Bos taurus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
133 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
134 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
135 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
136 <when value="gorilla_gorilla">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
137 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
138 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
139 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
140 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
141 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
142 <when value="callithrix_jacchus">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
143 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
144 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
145 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
146 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
147 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
148 <when value="ornithorhynchus_anatinus">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
149 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
150 <option value="mus_musculus">Mus musculus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
151 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
152 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
153 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
154 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
155 <when value="homo_sapiens">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
156 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
157 <option value="felis_catus">Felis catus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
158 <option value="rattus_norvegicus">Rattus norvegicus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
159 <option value="monodelphis_domestica">Monodelphis domestica</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
160 <option value="mus_musculus">Mus musculus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
161 <option value="canis_familiaris">Canis familiaris</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
162 <option value="oryctolagus_cuniculus">Oryctolagus cuniculus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
163 <option value="equus_caballus">Equus caballus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
164 <option value="gallus_gallus">Gallus gallus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
165 <option value="macaca_mulatta">Macaca mulatta</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
166 <option value="pongo_abelii">Pongo abelii</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
167 <option value="sus_scrofa">Sus scrofa</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
168 <option value="gorilla_gorilla">Gorilla gorilla</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
169 <option value="callithrix_jacchus">Callithrix jacchus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
170 <option value="ornithorhynchus_anatinus">Ornithorhynchus anatinus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
171 <option value="pan_troglodytes">Pan troglodytes</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
172 <option value="bos_taurus">Bos taurus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
173 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
174 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
175 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
176 <when value="anolis_carolinensis">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
177 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
178 <option value="gallus_gallus">Gallus gallus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
179 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
180 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
181 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
182 <when value="pan_troglodytes">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
183 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
184 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
185 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
186 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
187 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
188 <when value="bos_taurus">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
189 <param name="species2" type="select" label="Species2">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
190 <option value="sus_scrofa">Sus scrofa</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
191 <option value="mus_musculus">Mus musculus</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
192 <option value="homo_sapiens">Homo sapiens</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
193 <filter type="sort_by"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
194 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
195 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
196 </conditional>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
197 <param name="filter" type="select" label="Gene filter">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
198 <option value="false">Use all genes</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
199 <option value="true">Use only protein-coding genes</option>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
200 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
201 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
202 <when value="upload">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
203 <param name="species1" type="text" size="40" label="Species1 (latin name with underline)">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
204 <validator type="expression" message="Please replace any white spaces with underlines">value.find(' ')==-1</validator>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
205 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
206 <param name="species2" type="text" size="40" label="Species2 (latin name with underline)">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
207 <validator type="expression" message="Please replace any white spaces with underlines">value.find(' ')==-1</validator>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
208 </param>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
209 <param format="tabular" name="inputSyntenyRegions" type="data" label="Synteny Regions (e.g. from ENSEMBL)" help="Dataset missing? See TIP below."/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
210 <param format="tabular" name="inputHomologousGenes" type="data" label="Orthologous Genes (e.g. from ENSEMBL)" help="Dataset missing? See TIP below."/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
211 </when>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
212 </conditional>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
213
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
214 </inputs>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
215 <outputs>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
216 <data format="tabular" name="inputSyntenyRegions" label="ENSEMBL synteny regions">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
217 <filter>source['source_select'] == "ensembl"</filter>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
218 </data>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
219 <data format="tabular" name="inputHomologousGenes" label="ENSEMBL orthologous genes">
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
220 <filter>source['source_select'] == "ensembl"</filter>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
221 </data>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
222
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
223 <data format="tabular" name="out_file1" label="Gene mapping"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
224 <data format="tabular" name="out_file2" label="Refined Synteny regions"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
225 </outputs>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
226 <tests>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
227 <test>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
228 <param name="inputSyntenyRegions" value="hom_sapi-mus_musc-synteny-v70"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
229 <param name="inputHomologousGenes" value="hom_sapi-mus_musc-orthologs-v70.filtered"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
230 <param name="species1" value="homo_sapiens"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
231 <param name="species2" value="mus_musculus"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
232 <param name="filter" value="true"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
233 <!--<param name="header_lines" value="0"/>-->
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
234 <output name="out_file1" file="Gene_mapping1.out"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
235 <output name="out_file2" file="Refined_Synteny_regions2.out"/>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
236 </test>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
237 </tests>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
238
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
239 <help>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
240
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
241 .. class:: warningmark
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
242
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
243 If you are not downloading data directly from ENSEMBL, please make sure to bring your data into the correct format (see below).
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
244
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
245 .. class:: infomark
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
246
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
247 **TIP:** If your data is not TAB delimited, use *Text Manipulation-&gt;Convert*
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
248
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
249 .. class:: infomark
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
250
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
251 Species names should be given as latin names (e.g. Homo sapiens).
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
252
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
253 **TIP:** If you are interested only in the 1-to-1 ortholog mapping, use *Text Manipulation-&gt;Cut* on columns c3,c7 of the output Gene/IR mapping.
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
254
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
255 ----
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
256
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
257 **What it does**
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
258
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
259 SyntenyMapper uses two species' predefined macro-rearrangement blocks of common origin (e.g. synteny regions from ENSEMBL) and orthology assignments, both alignment-based, and combines them to create refined synteny regions with microrearrangement blocks and a 1-to-1 ortholog mapping.
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
260
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
261 It finds the longest blocks of conserved gene order within each synteny block and eliminates all orthology mappings with different gene neighbourhood. As a result, SyntenyMapper produces a list of segments with identical order of genes in both species, caused by micro-rearrangements. For visualization of this mapping, use SyntenyMapperVisualization. To utilize the mapping for feature track comparison between two species, use TrackMapper.
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
262
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
263 -----
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
264
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
265 **Syntax**
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
266
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
267 The SyntenyMapper allows you to identify long blocks of genes with conserved gene order in two organisms.
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
268
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
269 The mapping is based on previously determined long synteny regions and orthology pairs of genes.
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
270
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
271 First two comment lines (marked by a leading #) in the synteny file should name #Species1: and #Species2:, respectively. IDs should consist of five digits.
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
272 The synteny file should have the format (tab-separated):
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
273
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
274
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
275 +-----+-------------------+---------------+-------------+--------------------+---------------+-------------+-------------+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
276 |#ID |Chromosome_species1|Start_species1 |End_species1 |Chromosome_species2 |Start_species2 |End_species2 |Dir_species2 |
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
277 +-----+-------------------+---------------+-------------+--------------------+---------------+-------------+-------------+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
278
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
279
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
280 The orthologous genes file should have the format (tab-separated):
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
281
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
282
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
283 +---------+------------------+------------------------+-----------+---------+---------+----------+----------+-----------------+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
284 |#ID |ENSEMBL_ID |Name |Chromosome |Start |End |Direction | Identity |Species |
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
285 +---------+------------------+------------------------+-----------+---------+---------+----------+----------+-----------------+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
286
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
287
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
288 There should be two (or more) entries for each ID, describing pairs of genes that are orthologs.
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
289
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
290 -----
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
291
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
292 **Example**
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
293
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
294 These are sample lines from two example input files. If you are not downloading data directly from ENSEMBL (or reusing downloaded data), please make sure that it adheres to the above defined format.
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
295
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
296 The synteny file contains coordinates of large (e.g. whole-genome alignment based) synteny regions in both organisms and specifies the species names.
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
297
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
298 *Synteny file:*
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
299
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
300 +----------------------------------------------------------------------------------------------+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
301 |#Species1: homo_sapiens |
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
302 +----------------------------------------------------------------------------------------------+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
303 |#Species2: mus_musculus |
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
304 +-----+-----------------+------------+----------+-----------------+------------+----------+----+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
305 |#ID |Chromosome_human |Start_human |End_human |Chromosome_mouse |Start_mouse |End_mouse |Dir |
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
306 +-----+-----------------+------------+----------+-----------------+------------+----------+----+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
307 |44723|chr6 |155053083 |160101646 |chr17 |3113738 |7931992 |-1 |
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
308 +-----+-----------------+------------+----------+-----------------+------------+----------+----+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
309
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
310
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
311 The orthology file contains coordinates of genes of two species, coupled together by the same identifier to orthology pairs. Chromosomes can be named with "chr" prefix or without in both files.
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
312
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
313 *Orthology file:*
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
314
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
315 +---------+------------------+------------------------+-----------+---------+---------+----------+----------+-----------------+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
316 |#ID |ENSEMBL_ID |Name |Chromosome |Start |End |Direction | Identity |Species |
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
317 +---------+------------------+------------------------+-----------+---------+---------+----------+----------+-----------------+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
318 |33818986 |ENSRNOG00000050189|olfactory receptor Olr89|1 |174585043|174585993|1 |92.0 |rattus_norvegicus|
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
319 +---------+------------------+------------------------+-----------+---------+---------+----------+----------+-----------------+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
320 |33818986 |ENSMUSG00000073952|null |7 |103320401|103321360|1 |93.0 |mus_musculus |
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
321 +---------+------------------+------------------------+-----------+---------+---------+----------+----------+-----------------+
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
322
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
323 </help>
8a4190457eb7 Uploaded
s-kaufmann
parents:
diff changeset
324 </tool>