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comparison macros.xml @ 47:2892111d91f8 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 21:40:09 +0000
parents 64e2edfe7a2c
children
comparison
equal deleted inserted replaced
46:64e2edfe7a2c 47:2892111d91f8
49 <option value="-s">Only overlaps occurring on the **same** strand.</option> 49 <option value="-s">Only overlaps occurring on the **same** strand.</option>
50 <option value="-S">Only overlaps occurring on the **opposite** strand.</option> 50 <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
51 </param> 51 </param>
52 </xml> 52 </xml>
53 <xml name="seed"> 53 <xml name="seed">
54 <conditional name="seed"> 54 <param argument="-seed" type="integer" value="" min="0" optional="true" label="Seed" help="For reproducible 'randomness'"/>
55 <param name="seed_choose" type="select" label="Choose Seed?">
56 <option value="False" selected="true">Random Shuffling</option>
57 <option value="True">Choose fixed seed</option>
58 </param>
59 <when value="True">
60 <param argument="-seed" type="integer" value="12345" label="Enter Seed" />
61 </when>
62 <when value="False" />
63 </conditional>
64 </xml> 55 </xml>
65 <xml name="split"> 56 <xml name="split">
66 <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false" 57 <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false"
67 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." 58 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
68 help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." /> 59 help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
213 <option value="absmax">AbsMax - numeric only</option> 204 <option value="absmax">AbsMax - numeric only</option>
214 <option value="mean">Mean - numeric only</option> 205 <option value="mean">Mean - numeric only</option>
215 <option value="median">Median - numeric only</option> 206 <option value="median">Median - numeric only</option>
216 <option value="mode">Mode - numeric only</option> 207 <option value="mode">Mode - numeric only</option>
217 <option value="antimode">Antimode - numeric only</option> 208 <option value="antimode">Antimode - numeric only</option>
209 <option value="stdev">Standard deviation - numeric only</option>
210 <option value="sstdev">Sample standard deviation - numeric only</option>
218 <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option> 211 <option value="collapse">collapse (i.e., print a comma separated list) - numeric or text</option>
219 </xml> 212 </xml>
220 <xml name="additional_math_options"> 213 <xml name="additional_math_options">
221 <option value="count">Count - numeric or text</option> 214 <option value="count">Count - numeric or text</option>
222 <option value="count_disctinct">Count Distinct - numeric or text</option> 215 <option value="count_disctinct">Count Distinct - numeric or text</option>
223 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option> 216 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
224 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option> 217 <option value="distinct_sort_num">distinct sorted numerially (i.e., print a comma separated list) - numeric</option>
218 <option value="distinct_sort_num_desc">distinct sorted numerially descending (i.e., print a comma separated list) - numeric</option>
219 <option value="distinct_only">delimited list of only unique values - numeric or text</option>
220 <option value="first">just the first value in the column - numeric or text</option>
221 <option value="last">just the last value in the column - numeric or text</option>
225 </xml> 222 </xml>
226 <xml name="sorted"> 223 <xml name="sorted">
227 <!-- -sorted -g --> 224 <!-- -sorted -g -->
228 <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false" 225 <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false"
229 label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/> 226 label="For coordinate sorted input file the more efficient sweeping algorithm is enabled."/>