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comparison intersectBed.xml @ 54:b06c53665eb6 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 8e072170dd8f7b68fabbf29b1b0d7d14974b8b22"
author iuc
date Tue, 23 Mar 2021 20:21:30 +0000
parents 9a9f1a7abf54
children 7a06bb42dbb1
comparison
equal deleted inserted replaced
53:73e3ca75370a 54:b06c53665eb6
14 #if $modes == "None": 14 #if $modes == "None":
15 #set modes = '' 15 #set modes = ''
16 #end if 16 #end if
17 17
18 bedtools intersect 18 bedtools intersect
19 #if $inputA.is_of_type('bam'): 19 -a '${inputA}'
20 -abam '${inputA}'
21 #else:
22 -a '${inputA}'
23 #end if
24 20
25 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate': 21 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate':
26 -b '$reduce_or_iterate.inputB' 22 -b '$reduce_or_iterate.inputB'
27 #else: 23 #else:
28 -b 24 -b
51 #end if 47 #end if
52 $invert 48 $invert
53 $once 49 $once
54 $header 50 $header
55 $modes 51 $modes
56 $sorted 52 @SORTED@
57 #if str($sorted) != '':
58 #if str($reduce_or_iterate.reduce_or_iterate_selector) == 'iterate' and $reduce_or_iterate.inputB.is_of_type('bam'):
59 -g <(samtools view -H $reduce_or_iterate.inputB | tr ':' '\t' | grep SN | cut -f 3,5)
60 #else if str($reduce_or_iterate.reduce_or_iterate_selector) == 'reduce' and str($reduce_or_iterate.inputB) != 'None' and $reduce_or_iterate.inputB[0].is_of_type('bam'):
61 -g <(samtools view -H $reduce_or_iterate.inputB[0] | tr ':' '\t' | grep SN | cut -f 3,5)
62 #end if
63 #end if
64 $bed 53 $bed
65 $count 54 $count
66 > '${output}' 55 > '${output}'
67 ]]></command> 56 ]]></command>
68 <inputs> 57 <inputs>
122 <param name="count" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false" 111 <param name="count" argument="-c" type="boolean" truevalue="-c" falsevalue="" checked="false"
123 label="For each entry in A, report the number of overlaps with B." 112 label="For each entry in A, report the number of overlaps with B."
124 help="Reports 0 for A entries that have no overlap with B" /> 113 help="Reports 0 for A entries that have no overlap with B" />
125 <!-- -bed --> 114 <!-- -bed -->
126 <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false" 115 <param argument="-bed" type="boolean" truevalue="-bed" falsevalue="" checked="false"
127 label="When using BAM input (-abam), write output as BED instead of BAM." /> 116 label="When using BAM input, write output as BED instead of BAM." />
128 <!-- -sorted -g --> 117 <!-- -sorted -g -->
129 <param argument="-sorted" type="boolean" truevalue="-sorted" falsevalue="" checked="false" 118 <expand macro="sorted" />
130 label="For coordinate sorted input file the more efficient sweeping algorithm is enabled." />
131 <expand macro="print_header" /> 119 <expand macro="print_header" />
132 </inputs> 120 </inputs>
133 <outputs> 121 <outputs>
134 <data name="output" format_source="inputA" metadata_source="inputA"> 122 <data name="output" format_source="inputA" metadata_source="inputA">
135 <change_format> 123 <change_format>