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comparison macros.xml @ 17:44867b59dbf2 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174
author iuc
date Tue, 05 Sep 2017 15:40:14 -0400
parents 304a594a7ef6
children a8eabd2838f6
comparison
equal deleted inserted replaced
16:e0cec48a4695 17:44867b59dbf2
47 <xml name="split"> 47 <xml name="split">
48 <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" 48 <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue=""
49 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." 49 label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage."
50 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. (-split)" /> 50 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. (-split)" />
51 </xml> 51 </xml>
52 <xml name="genome"> 52 <xml name="input_conditional_genome_file">
53 <param format="tabular" name="genome" type="data" label="Genome file" /> 53 <conditional name="genome_file_opts">
54 <!--TODO: make use of: ${chromInfo} --> 54 <param name="genome_file_opts_selector" type="select" label="Genome file">
55 </xml> 55 <option value="loc" selected="True">Locally installed Genome file</option>
56 <option value="hist">Genome file from your history</option>
57 </param>
58 <when value="loc">
59 <param name="genome" type="select" multiple="false" label="Genome file">
60 <options from_data_table="__dbkeys__" />
61 </param>
62 </when>
63 <when value="hist">
64 <param name="genome" type="data" format="tabular" label="Genome file" />
65 </when>
66 </conditional>
67 </xml>
68 <token name="@GENOME_FILE@">
69 #if $genome_file_opts.genome_file_opts_selector == "loc":
70 '$genome_file_opts.genome.fields.len_path'
71 #elif $genome_file_opts.genome_file_opts_selector == "hist":
72 '$genome_file_opts.genome'
73 #end if
74 </token>
75 <token name="@GENOME_FILE_MAPBED@">
76 #if $genome.genome_choose == "-g":
77 #if $genome.genome_file_opts.genome_file_opts_selector == "loc":
78 -g '$genome.genome_file_opts.genome.fields.len_path'
79 #elif $genome.genome_file_opts.genome_file_opts_selector == "hist":
80 -g '$genome.genome_file_opts.genome'
81 #end if
82 #end if
83 </token>
84 <token name="@GENOME_FILE_MAKEWINDOWS@">
85 #if $type.type_select == "genome":
86 #if $type.genome_file_opts.genome_file_opts_selector == "loc":
87 -g '$type.genome_file_opts.genome.fields.len_path'
88 #elif $type.genome_file_opts.genome_file_opts_selector == "hist":
89 -g '$type.genome_file_opts.genome'
90 #end if
91 #end if
92 </token>
93 <token name="@GENOME_FILE_UNION@">
94 #if $empty.empty_selector == "-empty":
95 #if $empty.genome_file_opts.genome_file_opts_selector == "loc":
96 -g '$empty.genome_file_opts.genome.fields.len_path'
97 #elif $empty.genome_file_opts.genome_file_opts_selector == "hist":
98 -g '$empty.genome_file_opts.genome'
99 #end if
100 #end if
101 </token>
102 <token name="@GENOME_FILE_COVERAGE@">
103 #if $input_type.input_type_select == "bed":
104 -i '$input_type.input'
105 #if $input_type.genome_file_opts.genome_file_opts_selector == "loc":
106 -g '$input_type.genome_file_opts.genome.fields.len_path'
107 #elif $input_type.genome_file_opts.genome_file_opts_selector == "hist":
108 -g '$input_type.genome_file_opts.genome'
109 #end if
110 #elif $input_type.input_type_select == "bam":
111 -ibam '$input_type.input'
112 #end if
113 </token>
56 <xml name="closest_D_option"> 114 <xml name="closest_D_option">
57 <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue="" 115 <param name="iu" type="boolean" checked="false" truevalue="-iu" falsevalue=""
58 label="Ignore features in B that are upstream of features in A" 116 label="Ignore features in B that are upstream of features in A"
59 help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" /> 117 help="This option requires -D and follows its orientation rules for determining what is 'upstream'. (-iu)" />
60 118