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comparison mergeBed.xml @ 26:c0fbce5dc84a 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 10:13:20 -0400
parents a2d4c30ba2f9
children d279800f4ff9
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25:6c6963cf9136 26:c0fbce5dc84a
1 <tool id="bedtools_mergebed" name="MergeBED" version="@WRAPPER_VERSION@.1"> 1 <tool id="bedtools_mergebed" name="MergeBED" version="@WRAPPER_VERSION@.0">
2 <description>combine overlapping/nearby intervals into a single interval</description> 2 <description>combine overlapping/nearby intervals into a single interval</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" />
118 chr1 501 1000 + 118 chr1 501 1000 +
119 chr1 250 500 - 119 chr1 250 500 -
120 120
121 121
122 ========================================================================== 122 ==========================================================================
123 *-d* Controlling how close two features must be in order to merge 123 *-d* Controlling how close two features must be in order to merge
124 ========================================================================== 124 ==========================================================================
125 By default, only overlapping or book-ended features are combined into a new 125 By default, only overlapping or book-ended features are combined into a new
126 feature. However, one can force ``merge`` to combine more distant features 126 feature. However, one can force ``merge`` to combine more distant features
127 with the ``-d`` option. For example, were one to set ``-d`` to 1000, any 127 with the ``-d`` option. For example, were one to set ``-d`` to 1000, any
128 features that overlap or are within 1000 base pairs of one another will be 128 features that overlap or are within 1000 base pairs of one another will be
129 combined. 129 combined.
130 130
131 :: 131 ::
132 132
133 $ cat A.bed 133 $ cat A.bed
134 chr1 100 200 134 chr1 100 200
135 chr1 501 1000 135 chr1 501 1000
136 136
137 $ bedtools merge -i A.bed 137 $ bedtools merge -i A.bed
138 chr1 100 200 138 chr1 100 200
139 chr1 501 1000 139 chr1 501 1000
140 140
141 $ bedtools merge -i A.bed -d 1000 141 $ bedtools merge -i A.bed -d 1000