|
6
|
1 <tool id="svdetect_compare" name="Compare">
|
|
|
2
|
|
|
3 <description>structural variants between two samples</description>
|
|
|
4
|
|
|
5 <command interpreter="perl">SVDetect_compare.pl links2compare -conf '$config_file' -l '$log_file' -N '$sample_name.$reference_name'
|
|
|
6
|
|
|
7 #if $links2SV
|
|
|
8 -out1 '$common_sv_file'
|
|
|
9 -out2 '$sample_sv_file'
|
|
|
10 -out3 '$reference_sv_file'
|
|
|
11 #end if
|
|
|
12
|
|
|
13 #if $file_conversion.file_conversion_select=="convert" and $file_conversion.links2circos
|
|
|
14 -out4 '$common_circos_file'
|
|
|
15 -out5 '$sample_circos_file'
|
|
|
16 -out6 '$reference_circos_file'
|
|
|
17 #end if
|
|
|
18
|
|
|
19 #if $file_conversion.file_conversion_select=="convert" and $file_conversion.links2bed
|
|
|
20 -out7 '$common_bed_file'
|
|
|
21 -out8 '$sample_bed_file'
|
|
|
22 -out9 '$reference_bed_file'
|
|
|
23 #end if
|
|
|
24
|
|
|
25 </command>
|
|
|
26
|
|
|
27 <inputs>
|
|
|
28 <param name="sample_name" type="text" size="20" value="sample" label="Sample Name"/>
|
|
|
29 <param name="sample_read1_length" type="integer" size="10" value="50" label="Sample read 1 length (bp)"/>
|
|
|
30 <param name="sample_read2_length" type="integer" size="10" value="50" label="Sample read 2 length (bp)"/>
|
|
|
31 <param name="sample_mates_file" type="data" format="sv" label="Sample input file" help=".sv file"/>
|
|
|
32
|
|
|
33 <param name="reference_name" type="text" size="20" value="reference" label="Reference Name"/>
|
|
|
34 <param name="reference_read1_length" type="integer" size="10" value="50" label="Reference read 1 length (bp)"/>
|
|
|
35 <param name="reference_read2_length" type="integer" size="10" value="50" label="Reference read 2 length (bp)"/>
|
|
|
36 <param name="reference_mates_file" type="data" format="sv" label="Reference input file" help=".sv file"/>
|
|
|
37
|
|
|
38 <param name="min_overlap" type="float" size="10" value="0.05" label="Minimum overlap of links required as a fraction"/>
|
|
|
39 <param name="same_sv_type" label="Comparison of SVs with the same type only ?" type="boolean" truevalue="1" falsevalue="0" checked="True"/>
|
|
|
40
|
|
|
41 <param name="links2SV" label="Do you want to have filtered links in a tabulated file format showing significant SVs?" type="boolean" truevalue="1" falsevalue="0" checked="True"/>
|
|
|
42
|
|
|
43 <conditional name="file_conversion">
|
|
|
44 <param name="file_conversion_select" type="select" label="Output file conversion" help="Converts filtered links to Circos/BED files format for graphical view of SVs">
|
|
|
45 <option value="do_not_convert">No</option>
|
|
|
46 <option value="convert">Yes</option>
|
|
|
47 </param>
|
|
|
48 <when value="do_not_convert">
|
|
|
49 <!-- do nothing here -->
|
|
|
50 </when>
|
|
|
51 <when value="convert">
|
|
|
52 <param name="links2circos" label="Converts the link list to the Circos link format" type="boolean" truevalue="1" falsevalue="0" checked="True"/>
|
|
|
53 <param name="links2bed" label="Converts the link list to the UCSC BED format" type="boolean" truevalue="1" falsevalue="0" checked="False"/>
|
|
|
54 <param name="organism_id" type="text" size="10" value="hs" label="Organism ID"/>
|
|
|
55 <repeat name="color_code" title="Color-code" min="1" max="7">
|
|
|
56 <param name="color" type="select" label="Color">
|
|
|
57 <option value="grey">grey</option>
|
|
|
58 <option value="black">black</option>
|
|
|
59 <option value="blue">blue</option>
|
|
|
60 <option value="green">green</option>
|
|
|
61 <option value="purple">purple</option>
|
|
|
62 <option value="orange">orange</option>
|
|
|
63 <option value="red">red</option>
|
|
|
64 </param>
|
|
|
65 <param name="interval" type="text" value="1,3" label="Interval"/>
|
|
|
66 </repeat>
|
|
|
67 </when>
|
|
|
68 </conditional>
|
|
|
69 </inputs>
|
|
|
70
|
|
|
71
|
|
|
72
|
|
|
73 <outputs>
|
|
|
74 <data format="sv" name="common_sv_file" label="common.compared.sv">
|
|
|
75 <filter>links2SV is True</filter>
|
|
|
76 </data>
|
|
|
77 <data format="sv" name="sample_sv_file" label="${sample_name}.compared.sv">
|
|
|
78 <filter>links2SV is True</filter>
|
|
|
79 </data>
|
|
|
80 <data format="sv" name="reference_sv_file" label="${reference_name}.compared.sv">
|
|
|
81 <filter>links2SV is True</filter>
|
|
|
82 </data>
|
|
|
83
|
|
|
84 <data format="segdup" name="common_circos_file" label="common.compared.segdup">
|
|
|
85 <filter>(
|
|
|
86 file_conversion['file_conversion_select']=="convert" and
|
|
|
87 file_conversion['links2circos'] is True
|
|
|
88 )
|
|
|
89 </filter>
|
|
|
90 </data>
|
|
|
91 <data format="segdup" name="sample_circos_file" label="${sample_name}.compared.segdup">
|
|
|
92 <filter>(
|
|
|
93 file_conversion['file_conversion_select']=="convert" and
|
|
|
94 file_conversion['links2circos'] is True
|
|
|
95 )
|
|
|
96 </filter>
|
|
|
97 </data>
|
|
|
98 <data format="segdup" name="reference_circos_file" label="${reference_name}.compared.segdup">
|
|
|
99 <filter>(
|
|
|
100 file_conversion['file_conversion_select']=="convert" and
|
|
|
101 file_conversion['links2circos'] is True
|
|
|
102 )
|
|
|
103 </filter>
|
|
|
104 </data>
|
|
|
105
|
|
|
106 <data format="bed" name="common_bed_file" label="common.compared.bed">
|
|
|
107 <filter>(
|
|
|
108 file_conversion['file_conversion_select']=="convert" and
|
|
|
109 file_conversion['links2bed'] is True
|
|
|
110 )
|
|
|
111 </filter>
|
|
|
112 </data>
|
|
|
113 <data format="bed" name="sample_bed_file" label="${sample_name}.compared.bed">
|
|
|
114 <filter>(
|
|
|
115 file_conversion['file_conversion_select']=="convert" and
|
|
|
116 file_conversion['links2bed'] is True
|
|
|
117 )
|
|
|
118 </filter>
|
|
|
119 </data>
|
|
|
120 <data format="bed" name="reference_bed_file" label="${reference_name}.compared.bed">
|
|
|
121 <filter>(
|
|
|
122 file_conversion['file_conversion_select']=="convert" and
|
|
|
123 file_conversion['links2bed'] is True
|
|
|
124 )
|
|
|
125 </filter>
|
|
|
126 </data>
|
|
|
127
|
|
|
128 <data format="txt" name="log_file" label="${sample_name}.${reference_name}.svdetect_compare.log"/>
|
|
|
129 </outputs>
|
|
|
130
|
|
|
131
|
|
|
132
|
|
|
133 <configfiles>
|
|
|
134 <configfile name="config_file">
|
|
|
135 <general>
|
|
|
136 output_dir=$__new_file_path__/svdetect
|
|
|
137 </general>
|
|
|
138
|
|
|
139 #if $file_conversion.file_conversion_select == "convert"
|
|
|
140 #if $file_conversion.links2circos
|
|
|
141 <circos>
|
|
|
142 organism_id=${file_conversion.organism_id}
|
|
|
143 <colorcode>
|
|
|
144 #for $color_repeat in $file_conversion.color_code
|
|
|
145 ${color_repeat.color}=${color_repeat.interval}
|
|
|
146 #end for
|
|
|
147 </colorcode>
|
|
|
148 </circos>
|
|
|
149 #end if
|
|
|
150 #if $file_conversion.links2bed
|
|
|
151 <bed>
|
|
|
152 <colorcode>
|
|
|
153 #for $color_repeat in $file_conversion.color_code
|
|
|
154 #if str($color_repeat.color)== "grey"
|
|
|
155 190,190,190=${color_repeat.interval}
|
|
|
156 #end if
|
|
|
157 #if str($color_repeat.color)== "black"
|
|
|
158 0,0,0=${color_repeat.interval}
|
|
|
159 #end if
|
|
|
160 #if str($color_repeat.color)== "blue"
|
|
|
161 0,0,255=${color_repeat.interval}
|
|
|
162 #end if
|
|
|
163 #if str($color_repeat.color)== "green"
|
|
|
164 0,255,0=${color_repeat.interval}
|
|
|
165 #end if
|
|
|
166 #if str($color_repeat.color)== "purple"
|
|
|
167 153,50,205=${color_repeat.interval}
|
|
|
168 #end if
|
|
|
169 #if str($color_repeat.color)== "orange"
|
|
|
170 255,140,0=${color_repeat.interval}
|
|
|
171 #end if
|
|
|
172 #if str($color_repeat.color)== "red"
|
|
|
173 255,0,0=${color_repeat.interval}
|
|
|
174 #end if
|
|
|
175 #end for
|
|
|
176 </colorcode>
|
|
|
177 </bed>
|
|
|
178 #end if
|
|
|
179 #end if
|
|
|
180
|
|
|
181 <compare>
|
|
|
182 list_samples=${sample_name},${reference_name}
|
|
|
183 list_read_lengths=${sample_read1_length}-${sample_read2_length},${reference_read1_length}-${reference_read2_length}
|
|
|
184 sample_link_file=${sample_mates_file}
|
|
|
185 reference_link_file=${reference_mates_file}
|
|
|
186 min_overlap=${min_overlap}
|
|
|
187 same_sv_type=${same_sv_type}
|
|
|
188 sv_output=${links2SV}
|
|
|
189 #if $file_conversion.file_conversion_select == "convert"
|
|
|
190 circos_output=${$file_conversion.links2circos}
|
|
|
191 bed_output=${$file_conversion.links2bed}
|
|
|
192 #end if
|
|
|
193 </compare>
|
|
|
194
|
|
|
195 </configfile>
|
|
|
196 </configfiles>
|
|
|
197
|
|
|
198 <help>
|
|
|
199 **What it does**
|
|
|
200
|
|
|
201 SVDetect - Version : 0.8
|
|
|
202
|
|
|
203 Comparison of clusters between two samples to get common or sample-specific SVs
|
|
|
204
|
|
|
205 This program is designed to compare filtered links between two anomalously mapped mate-pair/paired-end datasets
|
|
|
206 and to identify common and sample-specific SVs (like the usual sample/reference design).
|
|
|
207 Overlaps between coordinates of clusters and types of SVs are used as parameters of comparison.
|
|
|
208
|
|
|
209 Manual documentation available at the http://svdetect.sourceforge.net/Site/Manual.html
|
|
|
210
|
|
|
211 -----
|
|
|
212
|
|
|
213 .. class:: infomark
|
|
|
214
|
|
|
215 Contact Bruno Zeitouni (bruno.zeitouni@curie.fr) for any questions or concerns about the Galaxy implementation of SVDetect.
|
|
|
216 </help>
|
|
|
217
|
|
|
218 </tool>
|
