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comparison intersectBed.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 1133660b0f9d
children 9224d51be786
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41:c96688f1746d 42:d279800f4ff9
35 $count 35 $count
36 > '${output}' 36 > '${output}'
37 ]]> 37 ]]>
38 </command> 38 </command>
39 <inputs> 39 <inputs>
40 <param format="bed,bam,vcf,gff,gff3" name="inputA" type="data" label="File A to intersect with B" help="BAM/BED/GFF/VCF format" /> 40 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="File A to intersect with B" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format" />
41 <conditional name="reduce_or_iterate"> 41 <conditional name="reduce_or_iterate">
42 <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'> 42 <param name='reduce_or_iterate_selector' type='select' label='Combined or separate output files'>
43 <option value='iterate' selected='true'>One output file per 'input B' file</option> 43 <option value='iterate' selected='true'>One output file per 'input B' file</option>
44 <option value='reduce'>Single output containing intersections of any 'input B' lines with A </option> 44 <option value='reduce'>Single output containing intersections of any 'input B' lines with A </option>
45 </param> 45 </param>
46 <when value='iterate'> 46 <when value='iterate'>
47 <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" 47 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data"
48 label="File(s) B to intersect with A" help="BAM/BED/GFF/VCF format"/> 48 label="File(s) B to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
49 </when> 49 </when>
50 <when value='reduce'> 50 <when value='reduce'>
51 <param format="bam,bed,gff,gff3,vcf" name="inputB" type="data" multiple="true" 51 <param format="bam,@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" multiple="true"
52 label="File(s) B to intersect with A" help="BAM/BED/GFF/VCF format"/> 52 label="File(s) B to intersect with A" help="BAM/@STD_BEDTOOLS_INPUT_LABEL@ format"/>
53 </when> 53 </when>
54 </conditional> 54 </conditional>
55 <expand macro="strand2" /> 55 <expand macro="strand2" />
56 <param name="overlap_mode" type="select" multiple="True" label="What should be written to the output file?"> 56 <param name="overlap_mode" type="select" multiple="True" label="What should be written to the output file?">
57 <option value="-wa" selected="True">Write the original entry in A for each overlap (-wa)</option> 57 <option value="-wa" selected="True">Write the original entry in A for each overlap (-wa)</option>
110 </tests> 110 </tests>
111 <help> 111 <help>
112 <![CDATA[ 112 <![CDATA[
113 **What it does** 113 **What it does**
114 114
115 By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. bedtools intersect allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. bedtools intersect works with both BED/GFF/VCF and BAM files as input. 115 By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. bedtools intersect allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. bedtools intersect works with both @STD_BEDTOOLS_INPUT_LABEL@ and BAM files as input.
116 116
117 .. image:: $PATH_TO_IMAGES/intersect-glyph.png 117 .. image:: $PATH_TO_IMAGES/intersect-glyph.png
118 118
119 .. class:: infomark 119 .. class:: infomark
120 120