Mercurial > repos > iuc > bedtools
comparison mergeBed.xml @ 2:457b09031d57 draft
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author | iuc |
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date | Tue, 19 May 2015 07:05:36 -0400 |
parents | 82aac94b06c3 |
children | 2cd7e321d259 |
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1:82aac94b06c3 | 2:457b09031d57 |
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1 <tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.0"> | 1 <tool id="bedtools_mergebed" name="Merge BED files" version="@WRAPPER_VERSION@.1"> |
2 <description>(mergeBed)</description> | 2 <description>(mergeBed)</description> |
3 <macros> | 3 <macros> |
4 <import>macros.xml</import> | 4 <import>macros.xml</import> |
5 </macros> | 5 </macros> |
6 <expand macro="requirements" /> | 6 <expand macro="requirements" /> |
10 mergeBed | 10 mergeBed |
11 -i "${input}" | 11 -i "${input}" |
12 $strand | 12 $strand |
13 -d $distance | 13 -d $distance |
14 $header | 14 $header |
15 @C_AND_O_ARGUMENT@ | |
15 > "${output}" | 16 > "${output}" |
16 ]]> | 17 ]]> |
17 </command> | 18 </command> |
18 <inputs> | 19 <inputs> |
19 <param name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF file"/> | 20 <param name="input" format="bam,bed,gff,vcf" type="data" label="Sort the following BAM/BED/VCF/GFF file"/> |
25 </param> | 26 </param> |
26 <param name="distance" type="integer" value="0" | 27 <param name="distance" type="integer" value="0" |
27 label="Maximum distance between features allowed for features to be merged" | 28 label="Maximum distance between features allowed for features to be merged" |
28 help="That is, overlapping and/or book-ended features are merged. (-d)"/> | 29 help="That is, overlapping and/or book-ended features are merged. (-d)"/> |
29 <expand macro="print_header" /> | 30 <expand macro="print_header" /> |
30 <expand macro="choose_columns" /> | 31 <expand macro="c_and_o_argument" /> |
31 <expand macro="choose_operations"> | |
32 <expand macro="math_options" /> | |
33 <expand macro="additional_math_options" /> | |
34 </expand> | |
35 </inputs> | 32 </inputs> |
36 <outputs> | 33 <outputs> |
37 <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/> | 34 <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/> |
38 </outputs> | 35 </outputs> |
39 <tests> | 36 <tests> |
53 </test> | 50 </test> |
54 <test> | 51 <test> |
55 <param name="input" value="mergedBed4.bed" ftype="bed" /> | 52 <param name="input" value="mergedBed4.bed" ftype="bed" /> |
56 <param name="distance" value="1000" /> | 53 <param name="distance" value="1000" /> |
57 <output name="output" file="mergedBed_result4.bed" ftype="bed" /> | 54 <output name="output" file="mergedBed_result4.bed" ftype="bed" /> |
55 </test> | |
56 <test> | |
57 <param name="input" value="mergedBed4.bed" ftype="bed" /> | |
58 <param name="distance" value="1000" /> | |
59 <repeat name="c_and_o_argument_repeat"> | |
60 <param name="col" value="1"/> | |
61 <param name="operation" value="count"/> | |
62 </repeat> | |
63 <output name="output" file="mergedBed_result5.bed" ftype="bed" /> | |
58 </test> | 64 </test> |
59 </tests> | 65 </tests> |
60 <help> | 66 <help> |
61 <![CDATA[ | 67 <![CDATA[ |
62 **What it does** | 68 **What it does** |
90 chr1 100 500 | 96 chr1 100 500 |
91 chr1 501 1000 | 97 chr1 501 1000 |
92 | 98 |
93 | 99 |
94 ========================================================================== | 100 ========================================================================== |
95 *-s* Enforcing "strandedness" | 101 *-s* Enforcing "strandedness" |
96 ========================================================================== | 102 ========================================================================== |
97 The ``-s`` option will only merge intervals that are overlapping/bookended | 103 The ``-s`` option will only merge intervals that are overlapping/bookended |
98 *and* are on the same strand. | 104 *and* are on the same strand. |
99 | 105 |
100 :: | 106 :: |
107 | 113 |
108 $ bedtools merge -i A.bed -s | 114 $ bedtools merge -i A.bed -s |
109 chr1 100 250 + | 115 chr1 100 250 + |
110 chr1 501 1000 + | 116 chr1 501 1000 + |
111 chr1 250 500 - | 117 chr1 250 500 - |
112 | |
113 | |
114 ========================================================================== | |
115 *-n* Reporting the number of features that were merged | |
116 ========================================================================== | |
117 The -n option will report the number of features that were combined from the | |
118 original file in order to make the newly merged feature. If a feature in the | |
119 original file was not merged with any other features, a "1" is reported. | |
120 | |
121 :: | |
122 | |
123 $ cat A.bed | |
124 chr1 100 200 | |
125 chr1 180 250 | |
126 chr1 250 500 | |
127 chr1 501 1000 | |
128 | |
129 $ bedtools merge -i A.bed -n | |
130 chr1 100 500 3 | |
131 chr1 501 1000 1 | |
132 | 118 |
133 | 119 |
134 ========================================================================== | 120 ========================================================================== |
135 *-d* Controlling how close two features must be in order to merge | 121 *-d* Controlling how close two features must be in order to merge |
136 ========================================================================== | 122 ========================================================================== |
152 | 138 |
153 $ bedtools merge -i A.bed -d 1000 | 139 $ bedtools merge -i A.bed -d 1000 |
154 chr1 100 200 1000 | 140 chr1 100 200 1000 |
155 | 141 |
156 | 142 |
157 ============================================================= | |
158 *-nms* Reporting the names of the features that were merged | |
159 ============================================================= | |
160 Occasionally, one might like to know that names of the features that were | |
161 merged into a new feature. The ``-nms`` option will add an extra column to the | |
162 ``merge`` output which lists (separated by semicolons) the names of the | |
163 merged features. | |
164 | |
165 :: | |
166 | |
167 $ cat A.bed | |
168 chr1 100 200 A1 | |
169 chr1 150 300 A2 | |
170 chr1 250 500 A3 | |
171 | |
172 $ bedtools merge -i A.bed -nms | |
173 chr1 100 500 A1,A2,A3 | |
174 | |
175 | |
176 =============================================================== | |
177 *-scores* Reporting the scores of the features that were merged | |
178 =============================================================== | |
179 Similarly, we might like to know that scores of the features that were | |
180 merged into a new feature. Enter the ``-scores`` option. One can specify | |
181 how the scores from each overlapping interval should be reported. | |
182 | |
183 :: | |
184 | |
185 $ cat A.bed | |
186 chr1 100 200 A1 1 | |
187 chr1 150 300 A2 2 | |
188 chr1 250 500 A3 3 | |
189 | |
190 $ bedtools merge -i A.bed -scores mean | |
191 chr1 100 500 2 | |
192 | |
193 $ bedtools merge -i A.bed -scores max | |
194 chr1 100 500 3 | |
195 | |
196 $ bedtools merge -i A.bed -scores collapse | |
197 chr1 100 500 1,2,3 | |
198 | |
199 @REFERENCES@ | 143 @REFERENCES@ |
200 ]]> | 144 ]]> |
201 </help> | 145 </help> |
202 <expand macro="citations" /> | 146 <expand macro="citations" /> |
203 </tool> | 147 </tool> |