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comparison coverageBed.xml @ 42:d279800f4ff9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
author iuc
date Thu, 26 Apr 2018 17:02:24 -0400
parents 58451dcd076d
children 71d71721695e
comparison
equal deleted inserted replaced
41:c96688f1746d 42:d279800f4ff9
37 #end if 37 #end if
38 > '$output' 38 > '$output'
39 ]]> 39 ]]>
40 </command> 40 </command>
41 <inputs> 41 <inputs>
42 <param format="bam,bed,gff,gff3,vcf" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/BED/GFF/VCF format" /> 42 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A (on which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
43 <conditional name="reduce_or_iterate"> 43 <conditional name="reduce_or_iterate">
44 <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'> 44 <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
45 <option value='iterate' selected='true'>One output file per 'input B' file</option> 45 <option value='iterate' selected='true'>One output file per 'input B' file</option>
46 <option value='reduce'>Single output containing results for all 'input B' files</option> 46 <option value='reduce'>Single output containing results for all 'input B' files</option>
47 </param> 47 </param>
48 <when value='iterate'> 48 <when value='iterate'>
49 <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" 49 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data"
50 label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format"/> 50 label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
51 </when> 51 </when>
52 <when value='reduce'> 52 <when value='reduce'>
53 <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true" 53 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" multiple="true"
54 label="File(s) B (for which coverage is calculated)" help="BAM/BED/GFF/VCF format"/> 54 label="File(s) B (for which coverage is calculated)" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
55 </when> 55 </when>
56 </conditional> 56 </conditional>
57 <expand macro="split" /> 57 <expand macro="split" />
58 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false" 58 <param name="strandedness" type="boolean" label="Force strandedness" truevalue="-s" falsevalue="" checked="false"
59 help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/> 59 help="Only report hits in B that overlap A on the same strand. By default, overlaps are reported without respect to strand (-s)"/>
67 label="Minimum overlap required as a fraction of A." 67 label="Minimum overlap required as a fraction of A."
68 help="Default is 1E-9 (i.e., 1bp). (-f)"> 68 help="Default is 1E-9 (i.e., 1bp). (-f)">
69 <sanitizer invalid_char=""> 69 <sanitizer invalid_char="">
70 <valid initial="string.digits"><add value=",."/></valid> 70 <valid initial="string.digits"><add value=",."/></valid>
71 </sanitizer> 71 </sanitizer>
72 </param> 72 </param>
73 <param name="overlap_b" type="text" 73 <param name="overlap_b" type="text"
74 label="Minimum overlap required as a fraction of B." 74 label="Minimum overlap required as a fraction of B."
75 help="Default is 1E-9 (i.e., 1bp). (-F)"> 75 help="Default is 1E-9 (i.e., 1bp). (-F)">
76 <sanitizer invalid_char=""> 76 <sanitizer invalid_char="">
77 <valid initial="string.digits"><add value=",."/></valid> 77 <valid initial="string.digits"><add value=",."/></valid>
78 </sanitizer> 78 </sanitizer>
79 </param> 79 </param>
80 <param name="reciprocal_overlap" type="boolean" checked="false" truevalue="-r" falsevalue="" 80 <param name="reciprocal_overlap" type="boolean" checked="false" truevalue="-r" falsevalue=""
81 label="Require that the fraction overlap be reciprocal for A AND B." 81 label="Require that the fraction overlap be reciprocal for A AND B."
82 help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B (-r)" /> 82 help="if -f is 0.90 and -r is used, this requires that B overlap 90% of A and A _also_ overlaps 90% of B (-r)" />
83 <param name="a_or_b" type="boolean" checked="false" truevalue="-e" falsevalue="" 83 <param name="a_or_b" type="boolean" checked="false" truevalue="-e" falsevalue=""
84 label="Require that the minimum fraction be satisfied for A OR B." 84 label="Require that the minimum fraction be satisfied for A OR B."