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comparison closestBed.xml @ 4:607c0576c6ab draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
author iuc
date Wed, 27 Jan 2016 15:15:59 -0500
parents 82aac94b06c3
children f8b7dc21b4ee
comparison
equal deleted inserted replaced
3:2cd7e321d259 4:607c0576c6ab
1 <tool id="bedtools_closestbed" name="ClosestBed" version="@WRAPPER_VERSION@.0"> 1 <tool id="bedtools_closestbed" name="ClosestBed" version="@WRAPPER_VERSION@.0">
2 <description></description> 2 <description>find the closest, potentially non-overlapping interval</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
18 $addition2.id 18 $addition2.id
19 #end if 19 #end if
20 $io 20 $io
21 -mdb $mdb 21 -mdb $mdb
22 -t $ties 22 -t $ties
23 #if $k:
24 -k $k
25 #end if
23 -a $inputA 26 -a $inputA
24 -b $inputBs 27 -b $inputBs
25 > $output 28 > $output
26 ]]> 29 ]]>
27 </command> 30 </command>
50 <option value="" selected="True">Do not report the distance et all.</option> 53 <option value="" selected="True">Do not report the distance et all.</option>
51 <option value="ref">Report distance with respect to the reference genome. B features with a lower (start, stop) are upstream. (-ref)</option> 54 <option value="ref">Report distance with respect to the reference genome. B features with a lower (start, stop) are upstream. (-ref)</option>
52 <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> 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>
53 <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> 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>
54 </param> 57 </param>
58 <when value="" />
55 <when value="ref"> 59 <when value="ref">
56 <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" 60 <expand macro="closest_D_option" />
57 label="Ignore features in B that are upstream of features in A"
58 help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" />
59
60 <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue=""
61 label="Ignore features in B that are downstream of features in A"
62 help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" />
63 </when> 61 </when>
64 <when value="a"> 62 <when value="a">
65 <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" 63 <expand macro="closest_D_option" />
66 label="Ignore features in B that are upstream of features in A"
67 help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" />
68
69 <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue=""
70 label="Ignore features in B that are downstream of features in A"
71 help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" />
72 </when> 64 </when>
73 <when value="b"> 65 <when value="b">
74 <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" 66 <expand macro="closest_D_option" />
75 label="Ignore features in B that are upstream of features in A"
76 help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" />
77
78 <param name="id" type="boolean" checked="false" truevalue="-id" falsevalue=""
79 label="Ignore features in B that are downstream of features in A"
80 help="This option requires -D and follows its orientation rules for determining what is 'downstream'. (-id)" />
81 </when> 67 </when>
82 </conditional> 68 </conditional>
69
70 <param name="k" type="integer" value="1" optional="True" min="1"
71 label="Report the k closest hits" help="(-k)"/>
83 72
84 <param name="io" type="boolean" checked="false" truevalue="-io" falsevalue="" 73 <param name="io" type="boolean" checked="false" truevalue="-io" falsevalue=""
85 label="Ignore features in B that overlap A" 74 label="Ignore features in B that overlap A"
86 help="That is, we want close, yet not touching features only. (-io)" /> 75 help="That is, we want close, yet not touching features only. (-io)" />
87 76
124 <param name="inputA" value="closestBed_c.bed" ftype="bed" /> 113 <param name="inputA" value="closestBed_c.bed" ftype="bed" />
125 <param name="inputB" value="closestBed_d.bed" ftype="bed" /> 114 <param name="inputB" value="closestBed_d.bed" ftype="bed" />
126 <param name="addition2_select" value="a" /> 115 <param name="addition2_select" value="a" />
127 <output name="output" file="closestBed_result5.bed" ftype="bed" /> 116 <output name="output" file="closestBed_result5.bed" ftype="bed" />
128 </test> 117 </test>
118 <test>
119 <param name="inputA" value="closestBedA.bed" ftype="bed" />
120 <param name="inputB" value="a.bed" ftype="bed" />
121 <param name="k" value="3" />
122 <output name="output" file="closestBed_result6.bed" ftype="bed" />
123 </test>
129 </tests> 124 </tests>
130 <help> 125 <help>
131 <![CDATA[ 126 <![CDATA[
132 **What it does** 127 **What it does**
133 128