Mercurial > repos > iuc > bedtools
annotate mergeBed.xml @ 39:3e38c9b3214f draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
| author | iuc |
|---|---|
| date | Wed, 01 Sep 2021 11:04:15 +0000 |
| parents | dde39ba9c031 |
| children | 7ab85ac5f64b |
| rev | line source |
|---|---|
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39
3e38c9b3214f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
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changeset
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1 <tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@" profile="@PROFILE@"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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2 <description>combine overlapping/nearby intervals into a single interval</description> |
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3e38c9b3214f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
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3 <expand macro="bio_tools" /> |
| 0 | 4 <macros> |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements" /> | |
| 8 <expand macro="stdio" /> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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changeset
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9 <command><![CDATA[ |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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10 mergeBed |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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11 -i '${input}' |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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12 $strand |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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13 -d $distance |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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14 $header |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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15 @C_AND_O_ARGUMENT@ |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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16 > '${output}' |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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17 ]]></command> |
| 0 | 18 <inputs> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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19 <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
| 1 | 20 <param name="strand" type="select" label="Calculation based on strandedness?"> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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21 <option value="" selected="true">Overlaps on either strand</option> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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22 <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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23 <option value="-S +">Force merge for forward strand only (-S +)</option> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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diff
changeset
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24 <option value="-S -">Force merge for reverse strand only (-S -)</option> |
| 1 | 25 </param> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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26 <param name="distance" argument="-d" type="integer" value="0" |
| 1 | 27 label="Maximum distance between features allowed for features to be merged" |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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28 help="That is, overlapping and/or book-ended features are merged"/> |
| 1 | 29 <expand macro="print_header" /> |
| 3 | 30 <expand macro="c_and_o_argument"> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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diff
changeset
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31 <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" /> |
| 3 | 32 </expand> |
| 0 | 33 </inputs> |
| 34 <outputs> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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diff
changeset
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35 <data name="output" format="bed" metadata_source="input" label="Merged ${input.name}"/> |
| 0 | 36 </outputs> |
| 37 <tests> | |
| 38 <test> | |
| 1 | 39 <param name="input" value="mergedBed1.bed" ftype="bed" /> |
| 40 <output name="output" file="mergedBed_result1.bed" ftype="bed" /> | |
| 0 | 41 </test> |
| 42 <test> | |
| 1 | 43 <param name="input" value="mergedBed2.bed" ftype="bed" /> |
| 0 | 44 <param name="strandedness" value="-s" /> |
| 1 | 45 <output name="output" file="mergedBed_result2.bed" ftype="bed" /> |
| 0 | 46 </test> |
| 47 <test> | |
| 1 | 48 <param name="input" value="mergedBed3.bed" ftype="bed" /> |
| 0 | 49 <param name="report_number" value="-n" /> |
| 1 | 50 <output name="output" file="mergedBed_result3.bed" ftype="bed" /> |
| 0 | 51 </test> |
| 52 <test> | |
| 1 | 53 <param name="input" value="mergedBed4.bed" ftype="bed" /> |
| 0 | 54 <param name="distance" value="1000" /> |
| 1 | 55 <output name="output" file="mergedBed_result4.bed" ftype="bed" /> |
| 0 | 56 </test> |
| 2 | 57 <test> |
| 58 <param name="input" value="mergedBed4.bed" ftype="bed" /> | |
| 59 <param name="distance" value="1000" /> | |
| 60 <repeat name="c_and_o_argument_repeat"> | |
| 61 <param name="col" value="1"/> | |
| 62 <param name="operation" value="count"/> | |
| 63 </repeat> | |
| 64 <output name="output" file="mergedBed_result5.bed" ftype="bed" /> | |
| 65 </test> | |
| 0 | 66 </tests> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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67 <help><![CDATA[ |
| 0 | 68 **What it does** |
| 69 | |
| 70 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features. | |
| 71 | |
| 72 | |
| 73 .. image:: $PATH_TO_IMAGES/merge-glyph.png | |
| 74 | |
| 75 | |
| 76 .. class:: warningmark | |
| 77 | |
| 78 bedtools merge requires that you presort your data by chromosome and then by start position. | |
| 79 | |
| 80 | |
| 81 ========================================================================== | |
| 82 Default behavior | |
| 83 ========================================================================== | |
| 84 By default, ``bedtools merge`` combines overlapping (by at least 1 bp) and/or | |
| 85 bookended intervals into a single, "flattened" or "merged" interval. | |
| 86 | |
| 87 :: | |
| 88 | |
| 89 $ cat A.bed | |
| 90 chr1 100 200 | |
| 91 chr1 180 250 | |
| 92 chr1 250 500 | |
| 93 chr1 501 1000 | |
| 94 | |
| 95 $ bedtools merge -i A.bed | |
| 96 chr1 100 500 | |
| 97 chr1 501 1000 | |
| 98 | |
| 99 | |
| 100 ========================================================================== | |
| 2 | 101 *-s* Enforcing "strandedness" |
| 0 | 102 ========================================================================== |
| 103 The ``-s`` option will only merge intervals that are overlapping/bookended | |
| 104 *and* are on the same strand. | |
| 105 | |
| 106 :: | |
| 107 | |
| 108 $ cat A.bed | |
| 109 chr1 100 200 a1 1 + | |
| 110 chr1 180 250 a2 2 + | |
| 111 chr1 250 500 a3 3 - | |
| 112 chr1 501 1000 a4 4 + | |
| 113 | |
| 114 $ bedtools merge -i A.bed -s | |
| 115 chr1 100 250 + | |
| 116 chr1 501 1000 + | |
| 117 chr1 250 500 - | |
| 118 | |
| 119 | |
| 120 ========================================================================== | |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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121 *-d* Controlling how close two features must be in order to merge |
| 0 | 122 ========================================================================== |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
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123 By default, only overlapping or book-ended features are combined into a new |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
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124 feature. However, one can force ``merge`` to combine more distant features |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
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changeset
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125 with the ``-d`` option. For example, were one to set ``-d`` to 1000, any |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
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126 features that overlap or are within 1000 base pairs of one another will be |
| 0 | 127 combined. |
| 128 | |
| 129 :: | |
| 130 | |
| 131 $ cat A.bed | |
| 132 chr1 100 200 | |
| 133 chr1 501 1000 | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
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changeset
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134 |
| 0 | 135 $ bedtools merge -i A.bed |
| 136 chr1 100 200 | |
| 137 chr1 501 1000 | |
| 138 | |
| 139 $ bedtools merge -i A.bed -d 1000 | |
| 140 chr1 100 200 1000 | |
| 141 | |
| 142 | |
| 143 @REFERENCES@ | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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144 ]]></help> |
| 0 | 145 <expand macro="citations" /> |
| 146 </tool> |