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comparison bedtools_genomecov/macros.xml @ 6:59d5cc7095f7 draft

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author jackcurragh
date Fri, 27 May 2022 11:58:00 +0000
parents f7beecae0315
children 4371d34bfd84
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5:f7beecae0315 6:59d5cc7095f7
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>
76 <when value="loc"> 76 <!-- <when value="loc">
77 <param name="genome" type="select" optional="@OPTIONAL@" multiple="false" label="Genome file"> 77 <param name="genome" type="select" optional="@OPTIONAL@" multiple="false" label="Genome file">
78 <options from_data_table="__dbkeys__" /> 78 <options from_data_table="__dbkeys__" />
79 </param> 79 </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'