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comparison macros.xml @ 12:c782e0edc4f1 draft default tip

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author bgruening
date Thu, 19 Jun 2014 10:12:00 -0400
parents e526617a6bb9
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11:e526617a6bb9 12:c782e0edc4f1
1 <macros> 1 <macros>
2 <xml name="requirements">
3 <requirements>
4 <requirement type="package" version="2.19.1">bedtools</requirement>
5 </requirements>
6 <version_command>bedtools --version</version_command>
7 </xml>
8 <token name="@WRAPPER_VERSION@">2.19</token>
2 <xml name="stdio"> 9 <xml name="stdio">
3 <stdio> 10 <stdio>
4 <!-- Anything other than zero is an error --> 11 <!-- Anything other than zero is an error -->
5 <exit_code range="1:" /> 12 <exit_code range="1:" />
6 <exit_code range=":-1" /> 13 <exit_code range=":-1" />
27 <param name="seed" type="integer" value="12345" label="Enter Seed" /> 34 <param name="seed" type="integer" value="12345" label="Enter Seed" />
28 </when> 35 </when>
29 </conditional> 36 </conditional>
30 </xml> 37 </xml>
31 <xml name="split"> 38 <xml name="split">
32 <param name="split" type="boolean" checked="true" truevalue="-split" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." 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." /> 39 <param name="split" type="boolean" checked="true" truevalue="-split" falsevalue=""
33 40 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
34 </xml> 41 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." />
35 <xml name="requirements">
36 <requirements>
37 <requirement type="package" version="2.19.1">bedtools</requirement>
38 </requirements>
39 <version_command>bedtools --version</version_command>
40 </xml> 42 </xml>
41 <xml name="genome"> 43 <xml name="genome">
42 <param format="bed,vcf,gff,gff3" name="genome" type="data" label="Genome file" /> 44 <param format="bed,vcf,gff,gff3" name="genome" type="data" label="Genome file" />
43 </xml> 45 </xml>
44 <xml name="addition"> 46 <xml name="addition">
49 </param> 51 </param>
50 <when value="b"> 52 <when value="b">
51 <param name="b" label="Give Value" type="integer" value="0" /> 53 <param name="b" label="Give Value" type="integer" value="0" />
52 </when> 54 </when>
53 <when value="lr"> 55 <when value="lr">
54 <param name="l" label="The number of base pairs to subtract from the start coordinate" type="integer" value="0" /> 56 <param name="l" label="The number of base pairs to subtract from the start coordinate" type="integer" value="0" />
55 <param name="r" label="The number of base pairs to add to the end coordinate" type="integer" value="0" /> 57 <param name="r" label="The number of base pairs to add to the end coordinate" type="integer" value="0" />
56 </when> 58 </when>
57 </conditional> 59 </conditional>
58 </xml> 60 </xml>
59 <xml name="math_options"> 61 <xml name="math_options">
60 <option value="min">Min - numeric only</option> 62 <option value="min">Min - numeric only</option>
69 <option value="count">Count - numeric or text</option> 71 <option value="count">Count - numeric or text</option>
70 <option value="count_disctinct">Count Distinct - numeric or text</option> 72 <option value="count_disctinct">Count Distinct - numeric or text</option>
71 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option> 73 <option value="distinct">distinct (i.e., print a comma separated list) - numeric or text</option>
72 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option> 74 <option value="concat">concat (i.e., print a comma separated list) - numeric or text</option>
73 </xml> 75 </xml>
74
75
76
77 <token name="@REFERENCES@"> 76 <token name="@REFERENCES@">
78 ------ 77 ------
79 78
80 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. 79 This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__.
81 If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__ 80 If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__