bedtools: closestBed.xml annotate

annotate closestBed.xml @ 37:ce3c7f062223 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"

author	iuc
date	Tue, 23 Mar 2021 20:23:14 +0000
parents	dde39ba9c031
children	3e38c9b3214f

rev	line source
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	1 <tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@">
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
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	27 -b
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	28 #for $file in $overlap_with.inputB:
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	29 '$file'
dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	30 #end for
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	31 #end if
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	32 > '$output'
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	33 ]]></command>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	34 <inputs>
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	35 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	36 <!-- 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	37 <conditional name="overlap_with">
26 95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 15 diff changeset	38 <param name="source" type="select" label="Overlap with: will you select a @STD_BEDTOOLS_INPUT_LABEL@ file from your history or use a built-in GFF file?" help="Built-in GFF files contain full annotation of a reference genome">
95a3b2c25bd1 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59 iuc parents: 15 diff changeset	39 <option value="history" selected="true">Use a @STD_BEDTOOLS_INPUT_LABEL@ file from the history</option>
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	40 <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	41 </param>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	42 <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	43 <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	44 <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	45 <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	46 <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	47 </options>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	48 </param>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	49 </when>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	50 <when value="history">
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	51 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="Select a @STD_BEDTOOLS_INPUT_LABEL@ file" />
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	52 </when>
b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	53 </conditional>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	54
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	55 <param name="ties" type="select"
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	56 label="How ties for closest feature should be handled"
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	57 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	58 <option value="all" selected="true">all - Report all ties (default)</option>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	59 <option value="first">first - Report the first tie that occurred in the B file</option>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	60 <option value="last">last - Report the last tie that occurred in the B file</option>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	61 </param>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	62
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	63 <expand macro="strand2" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	64
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	65 <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	66 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	67 help="The reported distance for overlapping features will be 0" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	68
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	69 <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	70 <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	71 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	72 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	73 <option value="" selected="true">Do not report the distance et all.</option>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	74 <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	75 <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	76 <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	77 </param>
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	78 <when value="" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	79 <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	80 <expand macro="closest_D_option" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	81 </when>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	82 <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	83 <expand macro="closest_D_option" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	84 </when>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	85 <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	86 <expand macro="closest_D_option" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	87 </when>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	88 </conditional>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	89
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	90 <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	91 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	92
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	93 <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	94 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	95 help="That is, we want close, yet not touching features only" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	96
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	97 <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	98 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	99 <option value="each" selected="true">Report closest records for each database. (-each)</option>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	100 <option value="all">Report closest records among all databases. (-all)</option>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	101 </param>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	102 </inputs>
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	103 <outputs>
5 f8b7dc21b4ee planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 33ef87ff883d6a5814ab5b4552d7b597711cae4c iuc parents: 4 diff changeset	104 <!-- Would like to use a nicer name, but since there are possibly many inputB datasets, falling back to ${on_string} -->
34 dde39ba9c031 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95 iuc parents: 32 diff changeset	105 <!-- <data name="output" format_source="inputA" 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	106 <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	107 </outputs>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	108 <tests>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	109 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	110 <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	111 <param name="source" value="history" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	112 <param name="inputB" value="closestBedB.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	113 <output name="output" file="closestBed_result1.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	114 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	115 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	116 <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	117 <param name="source" value="history" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	118 <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	119 <param name="addition" value="true" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	120 <output name="output" file="closestBed_result2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	121 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	122 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	123 <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	124 <param name="source" value="history" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	125 <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	126 <param name="addition" value="True" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	127 <param name="mdb" value="all" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	128 <output name="output" file="closestBed_result3.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	129 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	130 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	131 <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	132 <param name="source" value="history" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	133 <param name="inputB" value="closestBed_d.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	134 <param name="addition2_select" value="ref" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	135 <output name="output" file="closestBed_result4.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	136 </test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	137 <test>
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	138 <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	139 <param name="source" value="history" />
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	140 <param name="inputB" value="closestBed_d.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	141 <param name="addition2_select" value="a" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	142 <output name="output" file="closestBed_result5.bed" ftype="bed" />
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	143 </test>
4 607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316 iuc parents: 1 diff changeset	144 <test>
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="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	146 <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	147 <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	148 <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	149 <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	150 </test>
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	151 </tests>
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	152 <help><![CDATA[
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	153 What it does
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	154
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	155 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	156
1 82aac94b06c3 Uploaded iuc parents: 0 diff changeset	157 .. image:: $PATH_TO_IMAGES/closest-glyph.png
82aac94b06c3 Uploaded iuc parents: 0 diff changeset	158
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	159 @REFERENCES@
15 b73962f8fcbf planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit c5007eff737fcabb28fa726ac40f13a1cd4893c1 iuc parents: 11 diff changeset	160 ]]></help>
0 b8348686a0b9 Imported from capsule None iuc parents: diff changeset	161 <expand macro="citations" />
b8348686a0b9 Imported from capsule None iuc parents: diff changeset	162 </tool>

Mercurial > repos > iuc > bedtools

annotate closestBed.xml @ 37:ce3c7f062223 draft