Mercurial > repos > iuc > bedtools
annotate closestBed.xml @ 21:818cc3c02d70 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
| author | iuc |
|---|---|
| date | Sat, 27 Feb 2016 12:56:20 -0500 |
| parents | 102424c60727 |
| children | ac8b17b66663 |
| rev | line source |
|---|---|
| 8 | 1 <tool id="bedtools_closestbed" name="ClosestBed" version="@WRAPPER_VERSION@.0"> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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changeset
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2 <description>find the closest, potentially non-overlapping interval</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
| 10 #set inputBs = ' '.join( [ str( $file ) for $file in $inputB ] ) | |
| 11 | |
| 12 closestBed | |
| 13 $strand | |
| 14 $addition | |
| 15 #if $addition2.addition2_select: | |
| 16 -D $addition2.addition2_select | |
| 17 $addition2.iu | |
| 18 $addition2.id | |
| 19 #end if | |
| 20 $io | |
| 21 -mdb $mdb | |
| 22 -t $ties | |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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changeset
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23 #if $k: |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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24 -k $k |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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changeset
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25 #end if |
| 8 | 26 -a $inputA |
| 27 -b $inputBs | |
| 28 > $output | |
| 29 ]]> | |
| 30 </command> | |
| 31 <inputs> | |
| 32 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file"/> | |
| 33 <param format="bed,gff,vcf,gff3" name="inputB" type="data" multiple="True" label="overlap intervals in this BED/VCF/GFF file?"/> | |
| 34 | |
| 35 <param name="ties" type="select" | |
| 36 label="How ties for closest feature should be handled" | |
| 37 help="This occurs when two features in B have exactly the same overlap with a feature in A."> | |
| 38 <option value="all" selected="True">all - Report all ties (default)</option> | |
| 39 <option value="first">first - Report the first tie that occurred in the B file</option> | |
| 40 <option value="last">last - Report the last tie that occurred in the B file</option> | |
| 41 </param> | |
| 42 | |
| 43 <expand macro="strand2" /> | |
| 44 | |
| 45 <param name="addition" type="boolean" checked="false" truevalue="-d" falsevalue="" | |
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818cc3c02d70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
iuc
parents:
19
diff
changeset
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46 label="In addition to the closest feature in B, report its distance to A as an extra column" |
| 8 | 47 help="The reported distance for overlapping features will be 0. (-d)" /> |
| 48 | |
| 49 <conditional name="addition2"> | |
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818cc3c02d70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
iuc
parents:
19
diff
changeset
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50 <param name="addition2_select" type="select" |
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818cc3c02d70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
iuc
parents:
19
diff
changeset
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51 label="Add additional columns to report distance to upstream feature. Distance defintion" |
| 8 | 52 help="Like -d, report the closest feature in B, and its distance to A as an extra column. However unlike -d, use negative distances to report upstream features. (-D)"> |
| 53 <option value="" selected="True">Do not report the distance et all.</option> | |
| 54 <option value="ref">Report distance with respect to the reference genome. B features with a lower (start, stop) are upstream. (-ref)</option> | |
| 55 <option value="a">Report distance with respect to A. When A is on the - strand, "upstream" means B has a higher (start,stop). (-a)</option> | |
| 56 <option value="b">Report distance with respect to B. When B is on the - strand, "upstream" means A has a higher (start,stop). (-b)</option> | |
| 57 </param> | |
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102424c60727
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1cfbe7505ebac3b447c6ae0f0d76b42656496588
iuc
parents:
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diff
changeset
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58 <when value="" /> |
| 8 | 59 <when value="ref"> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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60 <expand macro="closest_D_option" /> |
| 8 | 61 </when> |
| 62 <when value="a"> | |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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63 <expand macro="closest_D_option" /> |
| 8 | 64 </when> |
| 65 <when value="b"> | |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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66 <expand macro="closest_D_option" /> |
| 8 | 67 </when> |
| 68 </conditional> | |
| 69 | |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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70 <param name="k" type="integer" value="1" optional="True" min="1" |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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71 label="Report the k closest hits" help="(-k)"/> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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72 |
| 8 | 73 <param name="io" type="boolean" checked="false" truevalue="-io" falsevalue="" |
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818cc3c02d70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
iuc
parents:
19
diff
changeset
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74 label="Ignore features in B that overlap A" |
| 8 | 75 help="That is, we want close, yet not touching features only. (-io)" /> |
| 76 | |
| 77 <param name="mdb" type="select" optional="True" | |
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21
818cc3c02d70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
iuc
parents:
19
diff
changeset
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78 label="How multiple databases are resolved" |
| 8 | 79 help="(-mdb)"> |
| 80 <option value="each" selected="True">Report closest records for each database. (-each)</option> | |
| 81 <option value="all">Report closest records among all databases. (-all)</option> | |
| 82 </param> | |
| 83 </inputs> | |
| 84 <outputs> | |
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818cc3c02d70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
iuc
parents:
19
diff
changeset
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85 <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} --> |
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818cc3c02d70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
iuc
parents:
19
diff
changeset
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86 <!-- <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> --> |
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818cc3c02d70
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c
iuc
parents:
19
diff
changeset
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87 <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${on_string}"/> |
| 8 | 88 </outputs> |
| 89 <tests> | |
| 90 <test> | |
| 91 <param name="inputA" value="closestBedA.bed" ftype="bed" /> | |
| 92 <param name="inputB" value="closestBedB.bed" ftype="bed" /> | |
| 93 <output name="output" file="closestBed_result1.bed" ftype="bed" /> | |
| 94 </test> | |
| 95 <test> | |
| 96 <param name="inputA" value="closestBed_a.bed" ftype="bed" /> | |
| 97 <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> | |
| 98 <param name="addition" value="True" /> | |
| 99 <output name="output" file="closestBed_result2.bed" ftype="bed" /> | |
| 100 </test> | |
| 101 <test> | |
| 102 <param name="inputA" value="closestBed_a.bed" ftype="bed" /> | |
| 103 <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> | |
| 104 <param name="addition" value="True" /> | |
| 105 <param name="mdb" value="all" /> | |
| 106 <output name="output" file="closestBed_result3.bed" ftype="bed" /> | |
| 107 </test> | |
| 108 <test> | |
| 109 <param name="inputA" value="closestBed_c.bed" ftype="bed" /> | |
| 110 <param name="inputB" value="closestBed_d.bed" ftype="bed" /> | |
| 111 <param name="addition2_select" value="ref" /> | |
| 112 <output name="output" file="closestBed_result4.bed" ftype="bed" /> | |
| 113 </test> | |
| 114 <test> | |
| 115 <param name="inputA" value="closestBed_c.bed" ftype="bed" /> | |
| 116 <param name="inputB" value="closestBed_d.bed" ftype="bed" /> | |
| 117 <param name="addition2_select" value="a" /> | |
| 118 <output name="output" file="closestBed_result5.bed" ftype="bed" /> | |
| 119 </test> | |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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120 <test> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
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121 <param name="inputA" value="closestBedA.bed" ftype="bed" /> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
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122 <param name="inputB" value="a.bed" ftype="bed" /> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
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123 <param name="k" value="3" /> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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diff
changeset
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124 <output name="output" file="closestBed_result6.bed" ftype="bed" /> |
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a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
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changeset
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125 </test> |
| 8 | 126 </tests> |
| 127 <help> | |
| 128 <![CDATA[ | |
| 129 **What it does** | |
| 130 | |
| 131 Similar to intersectBed, closestBed searches for overlapping features in A and B. In the event that no feature in B overlaps the current feature in A, closestBed will report the closest (that is, least genomic distance from the start or end of A) feature in B. For example, one might want to find which is the closest gene to a significant GWAS polymorphism. Note that closestBed will report an overlapping feature as the closest—that is, it does not restrict to closest non-overlapping feature. | |
| 132 | |
| 133 .. image:: $PATH_TO_IMAGES/closest-glyph.png | |
| 134 | |
| 135 | |
| 136 @REFERENCES@ | |
| 137 ]]> | |
| 138 </help> | |
| 139 <expand macro="citations" /> | |
| 140 </tool> |