Mercurial > repos > iuc > bedtools

comparison unionBedGraphs.xml @ 11:7308cc546a36 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
author iuc
date Mon, 17 Oct 2016 10:13:35 -0400
parents c78cf6fe3018
children 44867b59dbf2
comparison
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10:c78cf6fe3018 11:7308cc546a36
130 ------ 130 ------
131 131
132 **Examples using the Zero Coverage checkbox** 132 **Examples using the Zero Coverage checkbox**
133 133
134 Output example (*without* checking "Report regions with zero coverage"):: 134 Output example (*without* checking "Report regions with zero coverage")::
135 135
136 chr1 900 1000 0 60 0 136 chr1 900 1000 0 60 0
137 chr1 1000 1500 10 60 0 137 chr1 1000 1500 10 60 0
138 chr1 1500 1600 0 60 0 138 chr1 1500 1600 0 60 0
139 chr1 1700 1980 0 50 0 139 chr1 1700 1980 0 50 0
140 chr1 1980 2000 0 50 80 140 chr1 1980 2000 0 50 80
143 chr1 2070 2090 20 0 0 143 chr1 2070 2090 20 0 0
144 chr1 2090 2100 20 0 20 144 chr1 2090 2100 20 0 20
145 145
146 146
147 Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).:: 147 Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).::
148 148
149 chr1 0 900 0 0 0 (*) 149 chr1 0 900 0 0 0 (*)
150 chr1 900 1000 0 60 0 150 chr1 900 1000 0 60 0
151 chr1 1000 1500 10 60 0 151 chr1 1000 1500 10 60 0
152 chr1 1500 1600 0 60 0 152 chr1 1500 1600 0 60 0
153 chr1 1600 1700 0 0 0 (*) 153 chr1 1600 1700 0 0 0 (*)
155 chr1 1980 2000 0 50 80 155 chr1 1980 2000 0 50 80
156 chr1 2000 2050 20 50 80 156 chr1 2000 2050 20 50 80
157 chr1 2050 2070 20 0 80 157 chr1 2050 2070 20 0 80
158 chr1 2070 2090 20 0 0 158 chr1 2070 2090 20 0 0
159 chr1 2090 2100 20 0 20 159 chr1 2090 2100 20 0 20
160 chr1 2100 247249719 0 0 0 (*) 160 chr1 2100 247249719 0 0 0 (*)
161 161
162 162
163 ------ 163 ------
164 164
165 **Examples adjusting the "Filler value" for no-covered intervals** 165 **Examples adjusting the "Filler value" for no-covered intervals**
166 166
167 The default value is '0', but you can use any other value. 167 The default value is '0', but you can use any other value.
168 168
169 Output example with **filler = N/A**:: 169 Output example with **filler = N/A**::
170 170
171 chr1 900 1000 N/A 60 N/A 171 chr1 900 1000 N/A 60 N/A
172 chr1 1000 1500 10 60 N/A 172 chr1 1000 1500 10 60 N/A
173 chr1 1500 1600 N/A 60 N/A 173 chr1 1500 1600 N/A 60 N/A
174 chr1 1600 1700 N/A N/A N/A 174 chr1 1600 1700 N/A N/A N/A
175 chr1 1700 1980 N/A 50 N/A 175 chr1 1700 1980 N/A 50 N/A
202 **Non-numeric values** 202 **Non-numeric values**
203 203
204 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value. 204 The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value.
205 205
206 Input Example:: 206 Input Example::
207 207
208 File-1 File-2 208 File-1 File-2
209 chr1 200 300 Sample1 chr1 100 240 0.75 209 chr1 200 300 Sample1 chr1 100 240 0.75
210 chr1 400 450 Sample1 chr1 250 700 0.43 210 chr1 400 450 Sample1 chr1 250 700 0.43
211 chr1 530 600 Sample2 211 chr1 530 600 Sample2
212 212
213 Output Example:: 213 Output Example::
214 214
215 chr1 100 200 0 0.75 215 chr1 100 200 0 0.75
216 chr1 200 240 Sample1 0.75 216 chr1 200 240 Sample1 0.75
217 chr1 240 250 Sample1 0 217 chr1 240 250 Sample1 0
218 chr1 250 300 Sample1 0.43 218 chr1 250 300 Sample1 0.43
219 chr1 300 400 0 0.43 219 chr1 300 400 0 0.43