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comparison SVDetect_compare.xml @ 6:f6ccaaed3654 draft

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author bzeitouni
date Mon, 11 Jun 2012 12:31:19 -0400
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5:ba8c5e544948 6:f6ccaaed3654
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 &lt;general&gt;
136 output_dir=$__new_file_path__/svdetect
137 &lt;/general&gt;
138
139 #if $file_conversion.file_conversion_select == "convert"
140 #if $file_conversion.links2circos
141 &lt;circos&gt;
142 organism_id=${file_conversion.organism_id}
143 &lt;colorcode&gt;
144 #for $color_repeat in $file_conversion.color_code
145 ${color_repeat.color}=${color_repeat.interval}
146 #end for
147 &lt;/colorcode&gt;
148 &lt;/circos&gt;
149 #end if
150 #if $file_conversion.links2bed
151 &lt;bed&gt;
152 &lt;colorcode&gt;
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=${color_repeat.interval}
174 #end if
175 #end for
176 &lt;/colorcode&gt;
177 &lt;/bed&gt;
178 #end if
179 #end if
180
181 &lt;compare&gt;
182 list_samples=${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 &lt;/compare&gt;
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>