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comparison bedtools_genomecov/macros.xml @ 3:48e1c3a73761 draft

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author jackcurragh
date Fri, 27 May 2022 11:35:46 +0000
parents b63479816ebe
children d0638e3b9667
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2:3aa9416cc3b3 3:48e1c3a73761
65 <xml name="split"> 65 <xml name="split">
66 <param argument="-split" type="boolean" truevalue="-split" falsevalue="" checked="false" 66 <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." 67 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." /> 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." />
69 </xml> 69 </xml>
70 <xml name="input_conditional_genome_file" token_optional="false" token_help=""> 70 <!-- <xml name="input_conditional_genome_file" token_optional="false" token_help="">
71 <conditional name="genome_file_opts"> 71 <conditional name="genome_file_opts">
72 <param name="genome_file_opts_selector" type="select" label="Genome file" help="@HELP@"> 72 <param name="genome_file_opts_selector" type="select" label="Genome file" help="@HELP@">
73 <option value="loc" selected="true">Locally installed Genome file</option> 73 <option value="loc" selected="true">Locally installed Genome file</option>
74 <option value="hist">Genome file from your history</option> 74 <option value="hist">Genome file from your history</option>
75 </param> 75 </param>
80 </when> 80 </when>
81 <when value="hist"> 81 <when value="hist">
82 <param name="genome" type="data" optional="@OPTIONAL@" format="tabular" label="Genome file" /> 82 <param name="genome" type="data" optional="@OPTIONAL@" format="tabular" label="Genome file" />
83 </when> 83 </when>
84 </conditional> 84 </conditional>
85 </xml> 85 </xml> -->
86 <token name="@GENOME_FILE@"> 86 <token name="@GENOME_FILE@">
87 #if $genome_file_opts.genome 87 #if $genome_file_opts.genome
88 -g 88 -g
89 #if $genome_file_opts.genome_file_opts_selector == "loc": 89 #if $genome_file_opts.genome_file_opts_selector == "loc":
90 '$genome_file_opts.genome.fields.len_path' 90 '$genome_file_opts.genome.fields.len_path'