Mercurial > repos > iuc > bedtools
comparison mergeBed.xml @ 34:dde39ba9c031 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author | iuc |
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date | Mon, 29 Apr 2019 05:55:48 -0400 |
parents | 4f7a5ccd2ae9 |
children | 3e38c9b3214f |
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33:87ee588b3d45 | 34:dde39ba9c031 |
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1 <tool id="bedtools_mergebed" name="bedtools MergeBED" version="@WRAPPER_VERSION@"> | 1 <tool id="bedtools_mergebed" name="bedtools MergeBED" version="@TOOL_VERSION@"> |
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" /> |
7 <expand macro="stdio" /> | 7 <expand macro="stdio" /> |
8 <command> | 8 <command><![CDATA[ |
9 <![CDATA[ | 9 mergeBed |
10 mergeBed | 10 -i '${input}' |
11 -i "${input}" | 11 $strand |
12 $strand | 12 -d $distance |
13 -d $distance | 13 $header |
14 $header | 14 @C_AND_O_ARGUMENT@ |
15 @C_AND_O_ARGUMENT@ | 15 > '${output}' |
16 > "${output}" | 16 ]]></command> |
17 ]]> | |
18 </command> | |
19 <inputs> | 17 <inputs> |
20 <param name="input" format="bam,@STD_BEDTOOLS_INPUTS@" type="data" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/> | 18 <param name="input" argument="-i" type="data" format="bam,@STD_BEDTOOLS_INPUTS@" label="Sort the following BAM/@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
21 <param name="strand" type="select" label="Calculation based on strandedness?"> | 19 <param name="strand" type="select" label="Calculation based on strandedness?"> |
22 <option value="" selected="True">Overlaps on either strand</option> | 20 <option value="" selected="true">Overlaps on either strand</option> |
23 <option value="-s">Force strandedness. That is, only merge features that are the same strand.</option> | 21 <option value="-s">Force strandedness. That is, only merge features that are the same strand (-s)</option> |
24 <option value="-S +">Force merge for forward strand only.</option> | 22 <option value="-S +">Force merge for forward strand only (-S +)</option> |
25 <option value="-S -">Force merge for reverse strand only.</option> | 23 <option value="-S -">Force merge for reverse strand only (-S -)</option> |
26 </param> | 24 </param> |
27 <param name="distance" type="integer" value="0" | 25 <param name="distance" argument="-d" type="integer" value="0" |
28 label="Maximum distance between features allowed for features to be merged" | 26 label="Maximum distance between features allowed for features to be merged" |
29 help="That is, overlapping and/or book-ended features are merged. (-d)"/> | 27 help="That is, overlapping and/or book-ended features are merged"/> |
30 <expand macro="print_header" /> | 28 <expand macro="print_header" /> |
31 <expand macro="c_and_o_argument"> | 29 <expand macro="c_and_o_argument"> |
32 <param name="col" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" help="(-c)" /> | 30 <param name="col" argument="-c" type="data_column" data_ref="input" label="Specify the column(s) that should be summarized" /> |
33 </expand> | 31 </expand> |
34 </inputs> | 32 </inputs> |
35 <outputs> | 33 <outputs> |
36 <data format="bed" name="output" metadata_source="input" label="Merged ${input.name}"/> | 34 <data name="output" format="bed" metadata_source="input" label="Merged ${input.name}"/> |
37 </outputs> | 35 </outputs> |
38 <tests> | 36 <tests> |
39 <test> | 37 <test> |
40 <param name="input" value="mergedBed1.bed" ftype="bed" /> | 38 <param name="input" value="mergedBed1.bed" ftype="bed" /> |
41 <output name="output" file="mergedBed_result1.bed" ftype="bed" /> | 39 <output name="output" file="mergedBed_result1.bed" ftype="bed" /> |
63 <param name="operation" value="count"/> | 61 <param name="operation" value="count"/> |
64 </repeat> | 62 </repeat> |
65 <output name="output" file="mergedBed_result5.bed" ftype="bed" /> | 63 <output name="output" file="mergedBed_result5.bed" ftype="bed" /> |
66 </test> | 64 </test> |
67 </tests> | 65 </tests> |
68 <help> | 66 <help><![CDATA[ |
69 <![CDATA[ | |
70 **What it does** | 67 **What it does** |
71 | 68 |
72 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features. | 69 bedtools merge combines overlapping or "book-ended" features in an interval file into a single feature which spans all of the combined features. |
73 | 70 |
74 | 71 |
141 $ bedtools merge -i A.bed -d 1000 | 138 $ bedtools merge -i A.bed -d 1000 |
142 chr1 100 200 1000 | 139 chr1 100 200 1000 |
143 | 140 |
144 | 141 |
145 @REFERENCES@ | 142 @REFERENCES@ |
146 ]]> | 143 ]]></help> |
147 </help> | |
148 <expand macro="citations" /> | 144 <expand macro="citations" /> |
149 </tool> | 145 </tool> |