Mercurial > repos > iuc > bedtools
diff closestBed.xml @ 17:a2d4c30ba2f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
author | iuc |
---|---|
date | Sun, 21 Jun 2015 22:49:46 -0400 |
parents | 0d3aa592ce27 |
children | 102424c60727 |
line wrap: on
line diff
--- a/closestBed.xml Mon May 25 22:48:52 2015 -0400 +++ b/closestBed.xml Sun Jun 21 22:49:46 2015 -0400 @@ -1,5 +1,5 @@ <tool id="bedtools_closestbed" name="ClosestBed" version="@WRAPPER_VERSION@.0"> - <description></description> + <description>find the closest, potentially non-overlapping interval</description> <macros> <import>macros.xml</import> </macros> @@ -20,6 +20,9 @@ $io -mdb $mdb -t $ties + #if $k: + -k $k + #end if -a $inputA -b $inputBs > $output @@ -53,34 +56,19 @@ <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> </param> <when value="ref"> - <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" - label="Ignore features in B that are upstream of features in A" - help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" /> - - <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue="" - label="Ignore features in B that are downstream of features in A" - help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" /> + <expand macro="closest_D_option" /> </when> <when value="a"> - <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" - label="Ignore features in B that are upstream of features in A" - help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" /> - - <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue="" - label="Ignore features in B that are downstream of features in A" - help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" /> + <expand macro="closest_D_option" /> </when> <when value="b"> - <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" - label="Ignore features in B that are upstream of features in A" - help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" /> - - <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue="" - label="Ignore features in B that are downstream of features in A" - help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" /> + <expand macro="closest_D_option" /> </when> </conditional> + <param name="k" type="integer" value="1" optional="True" min="1" + label="Report the k closest hits" help="(-k)"/> + <param name="io" type="boolean" checked="false" truevalue="-io" falsevalue="" label="Ignore features in B that overlap A" help="That is, we want close, yet not touching features only. (-io)" /> @@ -126,6 +114,12 @@ <param name="addition2_select" value="a" /> <output name="output" file="closestBed_result5.bed" ftype="bed" /> </test> + <test> + <param name="inputA" value="closestBedA.bed" ftype="bed" /> + <param name="inputB" value="a.bed" ftype="bed" /> + <param name="k" value="3" /> + <output name="output" file="closestBed_result6.bed" ftype="bed" /> + </test> </tests> <help> <![CDATA[