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comparison closestBed.xml @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 9f6bd4c9479f
children
comparison
equal deleted inserted replaced
63:7411007544bf 64:f6c88d2e9ae5
1 <tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="bedtools_closestbed" name="bedtools ClosestBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>find the closest, potentially non-overlapping interval</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="bio_tools" /> 6 <expand macro="bio_tools" />
12 $addition 12 $addition
13 #if $addition2.addition2_select: 13 #if $addition2.addition2_select:
14 -D $addition2.addition2_select 14 -D $addition2.addition2_select
15 $addition2.iu 15 $addition2.iu
16 $addition2.id 16 $addition2.id
17 $addition2.fu
18 $addition2.fd
17 #end if 19 #end if
18 $io 20 $io
19 -mdb $mdb 21 -mdb $mdb
20 -t $ties 22 -t $ties
21 #if str($k): 23 #if str($k):
107 <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${on_string}" /> 109 <data name="output" format_source="inputA" metadata_source="inputA" label="Closest regions from ${on_string}" />
108 </outputs> 110 </outputs>
109 <tests> 111 <tests>
110 <test> 112 <test>
111 <param name="inputA" value="closestBedA.bed" ftype="bed" /> 113 <param name="inputA" value="closestBedA.bed" ftype="bed" />
112 <param name="source" value="history" /> 114 <param name="overlap_with|source" value="history" />
113 <param name="inputB" value="closestBedB.bed" ftype="bed" /> 115 <param name="overlap_with|inputB" value="closestBedB.bed" ftype="bed" />
114 <output name="output" file="closestBed_result1.bed" ftype="bed" /> 116 <output name="output" file="closestBed_result1.bed" ftype="bed" />
115 </test> 117 </test>
116 <test> 118 <test>
117 <param name="inputA" value="closestBed_a.bed" ftype="bed" /> 119 <param name="inputA" value="closestBed_a.bed" ftype="bed" />
118 <param name="source" value="history" /> 120 <param name="overlap_with|source" value="history" />
119 <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> 121 <param name="overlap_with|inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
120 <param name="addition" value="true" /> 122 <param name="addition" value="true" />
121 <output name="output" file="closestBed_result2.bed" ftype="bed" /> 123 <output name="output" file="closestBed_result2.bed" ftype="bed" />
122 </test> 124 </test>
123 <test> 125 <test>
124 <param name="inputA" value="closestBed_a.bed" ftype="bed" /> 126 <param name="inputA" value="closestBed_a.bed" ftype="bed" />
125 <param name="source" value="history" /> 127 <param name="overlap_with|source" value="history" />
126 <param name="inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" /> 128 <param name="overlap_with|inputB" value="closestBed_b1.bed,closestBed_b2.bed" ftype="bed" />
127 <param name="addition" value="True" /> 129 <param name="addition" value="True" />
128 <param name="mdb" value="all" /> 130 <param name="mdb" value="all" />
129 <output name="output" file="closestBed_result3.bed" ftype="bed" /> 131 <output name="output" file="closestBed_result3.bed" ftype="bed" />
130 </test> 132 </test>
131 <test> 133 <test>
132 <param name="inputA" value="closestBed_c.bed" ftype="bed" /> 134 <param name="inputA" value="closestBed_c.bed" ftype="bed" />
133 <param name="source" value="history" /> 135 <param name="overlap_with|source" value="history" />
134 <param name="inputB" value="closestBed_d.bed" ftype="bed" /> 136 <param name="overlap_with|inputB" value="closestBed_d.bed" ftype="bed" />
135 <param name="addition2_select" value="ref" /> 137 <param name="addition2|addition2_select" value="ref" />
136 <output name="output" file="closestBed_result4.bed" ftype="bed" /> 138 <output name="output" file="closestBed_result4.bed" ftype="bed" />
137 </test> 139 </test>
138 <test> 140 <test>
139 <param name="inputA" value="closestBed_c.bed" ftype="bed" /> 141 <param name="inputA" value="closestBed_c.bed" ftype="bed" />
140 <param name="source" value="history" /> 142 <param name="overlap_with|source" value="history" />
141 <param name="inputB" value="closestBed_d.bed" ftype="bed" /> 143 <param name="overlap_with|inputB" value="closestBed_d.bed" ftype="bed" />
142 <param name="addition2_select" value="a" /> 144 <param name="addition2|addition2_select" value="a" />
143 <output name="output" file="closestBed_result5.bed" ftype="bed" /> 145 <output name="output" file="closestBed_result5.bed" ftype="bed" />
144 </test> 146 </test>
145 <test> 147 <test>
146 <param name="inputA" value="closestBedA.bed" ftype="bed" /> 148 <param name="inputA" value="closestBedA.bed" ftype="bed" />
147 <param name="source" value="history" /> 149 <param name="overlap_with|source" value="history" />
148 <param name="inputB" value="a.bed" ftype="bed" /> 150 <param name="overlap_with|inputB" value="a.bed" ftype="bed" />
149 <param name="k" value="3" /> 151 <param name="k" value="3" />
150 <output name="output" file="closestBed_result6.bed" ftype="bed" /> 152 <output name="output" file="closestBed_result6.bed" ftype="bed" />
151 </test> 153 </test>
152 <test> 154 <test>
153 <param name="inputA" value="closestBedA.bed" ftype="bed" /> 155 <param name="inputA" value="closestBedA.bed" ftype="bed" />
154 <param name="source" value="data_table" /> 156 <param name="overlap_with|source" value="data_table" />
155 <param name="inputB" value="testid" /> 157 <param name="overlap_with|table" value="testid" />
156 <param name="k" value="3" /> 158 <param name="k" value="3" />
157 <output name="output" file="closestBed_result6.bed" ftype="bed" /> 159 <output name="output" file="closestBed_result6.bed" ftype="bed" />
158 </test> 160 </test>
159 </tests> 161 </tests>
160 <help><![CDATA[ 162 <help><![CDATA[