bedtools: closestBed.xml annotate

annotate closestBed.xml @ 15:b73962f8fcbf draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1

author	iuc
date	Wed, 05 Jul 2017 17:12:00 -0400
parents	7308cc546a36
children	95a3b2c25bd1

rev	line source
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	1 <tool id="bedtools_closestbed" name="ClosestBed" version="@WRAPPER_VERSION@.0">
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	2 <description>find the closest, potentially non-overlapping interval</description>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	3 <macros>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	4 <import>macros.xml</import>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	5 </macros>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	6 <expand macro="requirements" />
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	7 <expand macro="stdio" />
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	8 <command><![CDATA[
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	9 closestBed
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	10 $strand
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	11 $addition
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	12 #if $addition2.addition2_select:
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	13 -D $addition2.addition2_select
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	14 $addition2.iu
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	15 $addition2.id
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	16 #end if
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	17 $io
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	18 -mdb $mdb
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	19 -t $ties
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	20 #if str($k):
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	21 -k $k
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	22 #end if
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	23 -a '$inputA'
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	24 #if str($overlap_with.source) == "data_table":
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	25 -b '$overlap_with.table.fields.path'
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	26 #else
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	27 #set inputBs = "' '".join([str( $file ) for $file in $overlap_with.inputB])
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	28 -b '$inputBs'
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	29 #end if
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	30 > '$output'
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	31 ]]></command>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	32 <inputs>
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	33 <param name="inputA" type="data" format="bed,vcf,gff,gff3" label="BED/VCF/GFF file"/>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	34 <!-- overlap with file (inputB) -->
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	35 <conditional name="overlap_with">
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	36 <param name="source" type="select" label="Overlap with: will you select a BED/VCF/GFF file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	37 <option value="history" selected="true">Use a BED/VCF/GFF file from the history</option>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	38 <option value="data_table">Use a built-in GFF file</option>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	39 </param>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	40 <when value="data_table">
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	41 <param name="table" type="select" label="Select reference GFF" help="If your genome of interest is not listed, contact the Galaxy team">
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	42 <options from_data_table="all_gff">
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	43 <filter type="sort_by" column="2"/>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	44 <validator type="no_options" message="No files are available"/>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	45 </options>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	46 </param>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	47 </when>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	48 <when value="history">
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	49 <param name="inputB" type="data" format="bed,gff,vcf,gff3" multiple="true" label="Select a BED/VCF/GFF file" />
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	50 </when>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	51 </conditional>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	52
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	53 <param name="ties" type="select"
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	54 label="How ties for closest feature should be handled"
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	55 help="This occurs when two features in B have exactly the same overlap with a feature in A.">
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	56 <option value="all" selected="true">all - Report all ties (default)</option>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	57 <option value="first">first - Report the first tie that occurred in the B file</option>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	58 <option value="last">last - Report the last tie that occurred in the B file</option>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	59 </param>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	60
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	61 <expand macro="strand2" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	62
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	63 <param name="addition" argument="-d" type="boolean" truevalue="-d" falsevalue="" checked="false"
5 f8b7dc21b4ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c iuc parents: 4 diff changeset	64 label="In addition to the closest feature in B, report its distance to A as an extra column"
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	65 help="The reported distance for overlapping features will be 0" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	66
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	67 <conditional name="addition2">
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	68 <param name="addition2_select" argument="-D" type="select"
5 f8b7dc21b4ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c iuc parents: 4 diff changeset	69 label="Add additional columns to report distance to upstream feature. Distance defintion"
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	70 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">
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	71 <option value="" selected="true">Do not report the distance et all.</option>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	72 <option value="ref">Report distance with respect to the reference genome. B features with a lower (start, stop) are upstream. (-ref)</option>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	73 <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>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	74 <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>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	75 </param>
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	76 <when value="" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	77 <when value="ref">
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	78 <expand macro="closest_D_option" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	79 </when>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	80 <when value="a">
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	81 <expand macro="closest_D_option" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	82 </when>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	83 <when value="b">
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	84 <expand macro="closest_D_option" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	85 </when>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	86 </conditional>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	87
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	88 <param argument="-k" type="integer" min="1" value="1" optional="true"
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	89 label="Report the k closest hits" />
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	90
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	91 <param argument="-io" type="boolean" truevalue="-io" falsevalue="" checked="false"
5 f8b7dc21b4ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c iuc parents: 4 diff changeset	92 label="Ignore features in B that overlap A"
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	93 help="That is, we want close, yet not touching features only" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	94
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	95 <param argument="-mdb" type="select"
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	96 label="How multiple databases are resolved">
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	97 <option value="each" selected="true">Report closest records for each database. (-each)</option>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	98 <option value="all">Report closest records among all databases. (-all)</option>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	99 </param>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	100 </inputs>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	101 <outputs>
5 f8b7dc21b4ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c iuc parents: 4 diff changeset	102 <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} -->
f8b7dc21b4ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c iuc parents: 4 diff changeset	103 <!-- <data format_source="inputA" name="output" metadata_source="inputA" label="Closest regions from ${inputB[0].name} to ${inputA.name}"/> -->
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	104 <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${on_string}" />
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	105 </outputs>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	106 <tests>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	107 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	108 <param name="inputA" value="closestBedA.bed" ftype="bed" />
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	109 <param name="source" value="history" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	110 <param name="inputB" value="closestBedB.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	111 <output name="output" file="closestBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	112 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	113 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	114 <param name="inputA" value="closestBed_a.bed" ftype="bed" />
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	115 <param name="source" value="history" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	116 <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	117 <param name="addition" value="true" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	118 <output name="output" file="closestBed_result2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	119 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	120 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	121 <param name="inputA" value="closestBed_a.bed" ftype="bed" />
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	122 <param name="source" value="history" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	123 <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	124 <param name="addition" value="True" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	125 <param name="mdb" value="all" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	126 <output name="output" file="closestBed_result3.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	127 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	128 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	129 <param name="inputA" value="closestBed_c.bed" ftype="bed" />
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	130 <param name="source" value="history" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	131 <param name="inputB" value="closestBed_d.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	132 <param name="addition2_select" value="ref" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	133 <output name="output" file="closestBed_result4.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	134 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	135 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	136 <param name="inputA" value="closestBed_c.bed" ftype="bed" />
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	137 <param name="source" value="history" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	138 <param name="inputB" value="closestBed_d.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	139 <param name="addition2_select" value="a" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	140 <output name="output" file="closestBed_result5.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	141 </test>
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	142 <test>
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	143 <param name="inputA" value="closestBedA.bed" ftype="bed" />
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	144 <param name="source" value="history" />
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	145 <param name="inputB" value="a.bed" ftype="bed" />
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	146 <param name="k" value="3" />
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	147 <output name="output" file="closestBed_result6.bed" ftype="bed" />
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	148 </test>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	149 </tests>
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	150 <help><![CDATA[
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	151 What it does
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	152
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	153 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.
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	154
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	155 .. image:: $PATH_TO_IMAGES/closest-glyph.png
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	156
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	157 @REFERENCES@
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	158 ]]></help>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	159 <expand macro="citations" />
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	160 </tool>

Mercurial > repos > iuc > bedtools

annotate closestBed.xml @ 15:b73962f8fcbf draft