Mercurial > repos > iuc > bedtools
comparison intersectBed.xml @ 43:07e8b80f278c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
author | iuc |
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date | Fri, 01 Apr 2022 19:02:51 +0000 |
parents | 7ab85ac5f64b |
children | 64e2edfe7a2c |
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42:841fb4dc3ab3 | 43:07e8b80f278c |
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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"> |