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comparison intersectBed.xml @ 61:9f6bd4c9479f draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
author iuc
date Fri, 01 Apr 2022 19:00:48 +0000
parents 539958feb49c
children f6c88d2e9ae5
comparison
equal deleted inserted replaced
60:36d57dc82aa6 61:9f6bd4c9479f
1 <tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@" profile="@PROFILE@"> 1 <tool id="bedtools_intersectbed" name="bedtools Intersect intervals" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
2 <description>find overlapping intervals in various ways</description> 2 <description>find overlapping intervals in various ways</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" />
49 $invert 49 $invert
50 $once 50 $once
51 $header 51 $header
52 $modes 52 $modes
53 @SORTED@ 53 @SORTED@
54 @GENOME_FILE@
54 $bed 55 $bed
55 $count 56 $count
56 > '${output}' 57 > '${output}'
57 ]]></command> 58 ]]></command>
58 <inputs> 59 <inputs>
115 <!-- -bed --> 116 <!-- -bed -->
116 <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false" 117 <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
117 label="When using BAM input, write output as BED instead of BAM." /> 118 label="When using BAM input, write output as BED instead of BAM." />
118 <!-- -sorted -g --> 119 <!-- -sorted -g -->
119 <expand macro="sorted" /> 120 <expand macro="sorted" />
121 <expand macro="input_conditional_genome_file" optional="true" help="Only applies when used with -sorted option."/>
120 <expand macro="print_header" /> 122 <expand macro="print_header" />
121 </inputs> 123 </inputs>
122 <outputs> 124 <outputs>
123 <data name="output" format_source="inputA" metadata_source="inputA"> 125 <data name="output" format_source="inputA" metadata_source="inputA">
124 <change_format> 126 <change_format>
149 <conditional name="reduce_or_iterate"> 151 <conditional name="reduce_or_iterate">
150 <param name="reduce_or_iterate_selector" value="reduce" /> 152 <param name="reduce_or_iterate_selector" value="reduce" />
151 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" /> 153 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
152 </conditional> 154 </conditional>
153 <param name="overlap_mode" value="-wa,-wb" /> 155 <param name="overlap_mode" value="-wa,-wb" />
154 <param name="sorted" value="-sorted" /> 156 <param name="sorted" value="true" />
155 <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" /> 157 <output name="output" file="intersect-multiple-wa-wb.bed" ftype="bed" />
156 </test> 158 </test>
157 <test> 159 <test>
158 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" /> 160 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
159 <param name="inputA" value="intersect-query.bed" ftype="bed" /> 161 <param name="inputA" value="intersect-query.bed" ftype="bed" />
161 <param name="reduce_or_iterate_selector" value="reduce" /> 163 <param name="reduce_or_iterate_selector" value="reduce" />
162 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" /> 164 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
163 <param name="names" value="yes" /> 165 <param name="names" value="yes" />
164 </conditional> 166 </conditional>
165 <param name="overlap_mode" value="-wa,-wb" /> 167 <param name="overlap_mode" value="-wa,-wb" />
166 <param name="sorted" value="-sorted" /> 168 <param name="sorted" value="true" />
167 <output name="output" file="intersect-multiple-wa-wb-wnames.bed" ftype="bed" /> 169 <output name="output" file="intersect-multiple-wa-wb-wnames.bed" ftype="bed" />
168 </test> 170 </test>
169 <test> 171 <test>
170 <param name="inputA" value="intersect-query.bed" ftype="bed" /> 172 <param name="inputA" value="intersect-query.bed" ftype="bed" />
171 <conditional name="reduce_or_iterate"> 173 <conditional name="reduce_or_iterate">
172 <param name="reduce_or_iterate_selector" value="reduce" /> 174 <param name="reduce_or_iterate_selector" value="reduce" />
173 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" /> 175 <param name="inputB" value="intersect-d1.bed,intersect-d2.bed,intersect-d3.bed" ftype="bed" />
174 </conditional> 176 </conditional>
175 <param name="invert" value="-v" /> 177 <param name="invert" value="-v" />
176 <param name="sorted" value="-sorted" /> 178 <param name="sorted" value="true" />
177 <output name="output" file="intersect-multiple-invert.bed" ftype="bed" /> 179 <output name="output" file="intersect-multiple-invert.bed" ftype="bed" />
178 </test> 180 </test>
179 <test> 181 <test>
180 <param name="inputA" value="intersect-query.bed" ftype="bed" /> 182 <param name="inputA" value="intersect-query.bed" ftype="bed" />
181 <conditional name="reduce_or_iterate"> 183 <conditional name="reduce_or_iterate">
185 <param name="overlap_mode" value="-wa,-wb" /> 187 <param name="overlap_mode" value="-wa,-wb" />
186 <conditional name="fraction_cond"> 188 <conditional name="fraction_cond">
187 <param name="fraction_select" value="specify"/> 189 <param name="fraction_select" value="specify"/>
188 <param name="overlap" value="1.0" /> 190 <param name="overlap" value="1.0" />
189 </conditional> 191 </conditional>
190 <param name="sorted" value="-sorted" /> 192 <param name="sorted" value="true" />
191 <output name="output" file="intersect-multiple-fracA.bed" ftype="bed" /> 193 <output name="output" file="intersect-multiple-fracA.bed" ftype="bed" />
192 </test> 194 </test>
193 <test> 195 <test>
194 <param name="inputA" value="intersect-A.bed" ftype="bed" /> 196 <param name="inputA" value="intersect-A.bed" ftype="bed" />
195 <conditional name="reduce_or_iterate"> 197 <conditional name="reduce_or_iterate">