Mercurial > repos > iuc > bedtools
annotate windowBed.xml @ 11:7308cc546a36 draft
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 | 607c0576c6ab |
| children | fadebae7e69b |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bedtools_windowbed" name="WindowBed" version="@WRAPPER_VERSION@.0"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
parents:
1
diff
changeset
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2 <description>find overlapping intervals within a window around an interval</description> |
| 0 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 1 | 9 <![CDATA[ |
| 0 | 10 bedtools window |
| 11 #if $inputA.ext == "bam": | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
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12 -abam '$inputA' |
| 0 | 13 #else: |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
14 -a '$inputA' |
| 0 | 15 #end if |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
16 -b '$inputB' |
| 0 | 17 $bed |
| 18 $strandB | |
| 1 | 19 #if $addition.addition_select == 'window': |
| 20 -w $addition.w | |
| 0 | 21 #elif $addition.addition_select == 'lr': |
| 1 | 22 -l $addition.l |
| 23 -r $addition.r | |
| 0 | 24 #end if |
| 25 $original | |
| 26 $number | |
| 27 $nooverlaps | |
| 28 $header | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
|
29 > '$output' |
| 1 | 30 ]]> |
| 0 | 31 </command> |
| 32 <inputs> | |
| 33 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF/BAM file"/> | |
| 34 <param format="bed,gff,vcf,gff3" name="inputB" type="data" label="BED/VCF/GFF file"/> | |
| 1 | 35 <param name="bed" type="boolean" checked="false" truevalue="-bed" falsevalue="" |
| 36 label="When using BAM input, write output as BED. The default is to write output in BAM when using a bam file" | |
| 37 help="(-bed)" /> | |
| 0 | 38 <conditional name="addition"> |
| 39 <param name="addition_select" type="select" label="Choose what you want to do"> | |
| 1 | 40 <option value="window">Add Base pairs for **both** upstream and downstream of each entry in A when searching for overlaps in B</option> |
| 0 | 41 <option value="lr">Add Base pairs **separately** for upstream and downstream of each entry in A when searching for overlaps in B</option> |
| 42 </param> | |
| 1 | 43 <when value="window"> |
| 44 <param name="w" type="integer" value="1000" label="Base pairs to add upstream and downstream" /> | |
| 0 | 45 </when> |
| 46 <when value="lr"> | |
| 1 | 47 <param name="l" type="integer" value="1000" |
| 48 label="Base pairs added upstream (left) of each entry in A when searching for overlaps in B" | |
| 49 help="Allows one to create assymetrical “windows”. Default is 1000bp. (-l)" /> | |
| 50 <param name="r" type="integer" value="1000" | |
| 51 label="Base pairs added downstream (right) of each entry in A when searching for overlaps in B" | |
| 52 help="Allows one to create assymetrical “windows”. Default is 1000bp. (-r)" /> | |
| 0 | 53 </when> |
| 54 </conditional> | |
| 55 <param name="strandB" type="select" label="Calculation based on strandedness?"> | |
| 56 <option value="" selected="True">Report any hit in B</option> | |
| 57 <option value="-sm">Only report hits in B that overlap A on the **same** strand</option> | |
| 58 <option value="-Sm">Only report hits in B that overlap A on the **opposite** strand</option> | |
| 59 </param> | |
| 1 | 60 <param name="original" type="boolean" checked="false" truevalue="-u" falsevalue="" |
| 61 label="Write original A entry once if any overlaps found in B" | |
| 62 help="In other words, just report the fact at least one overlap was found in B. (-u)" /> | |
| 63 <param name="number" type="boolean" checked="false" truevalue="-c" falsevalue="" | |
| 64 label="For each entry in A, report the number of hits in B" | |
| 65 help="Reports 0 for A entries that have no overlap with B (-c)" /> | |
| 66 <param name="nooverlaps" type="boolean" checked="false" truevalue="-v" falsevalue="" | |
| 67 label="Only report those entries in A that have no overlaps with B" help="(-v)" /> | |
| 68 <expand macro="print_header" /> | |
| 0 | 69 </inputs> |
| 70 <outputs> | |
| 71 <data format_source="inputA" name="output" metadata_source="inputA" label=""/> | |
| 72 </outputs> | |
| 1 | 73 <tests> |
| 74 <test> | |
| 75 <param name="inputA" value="windowBedA.bed" ftype="bed" /> | |
| 76 <param name="inputB" value="windowBedB.bed" ftype="bed" /> | |
| 77 <output name="output" file="windowBed_result1.bed" ftype="bed" /> | |
| 78 </test> | |
| 79 <test> | |
| 80 <param name="inputA" value="windowBedA.bed" ftype="bed" /> | |
| 81 <param name="inputB" value="windowBedB.bed" ftype="bed" /> | |
| 82 <param name="addition_select" value="window" /> | |
| 83 <param name="w" value="5000" /> | |
| 84 <output name="output" file="windowBed_result2.bed" ftype="bed" /> | |
| 85 </test> | |
| 86 <test> | |
| 87 <param name="inputA" value="windowBedA.bed" ftype="bed" /> | |
| 88 <param name="inputB" value="windowBedB.bed" ftype="bed" /> | |
| 89 <param name="addition_select" value="lr" /> | |
| 90 <param name="l" value="200" /> | |
| 91 <param name="r" value="20000" /> | |
| 92 <output name="output" file="windowBed_result2.bed" ftype="bed" /> | |
| 93 </test> | |
| 94 </tests> | |
| 0 | 95 <help> |
| 1 | 96 <![CDATA[ |
| 0 | 97 **What it does** |
| 98 | |
| 99 Similar to bedtools intersect, window searches for overlapping features in A and B. However, window adds a specified number (1000, by default) of base pairs upstream and downstream of each feature in A. In effect, this allows features in B that are “near” features in A to be detected. | |
| 100 | |
| 101 .. image:: $PATH_TO_IMAGES/window-glyph.png | |
| 102 | |
| 103 @REFERENCES@ | |
| 1 | 104 ]]> |
| 0 | 105 </help> |
| 106 <expand macro="citations" /> | |
| 107 </tool> |