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comparison macros.xml @ 32:b0d5e752c0c5 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit a78ca56350b1fcf9d7de2a1112155c9bd0844348
author iuc
date Tue, 05 Sep 2017 09:51:56 -0400
parents 60ecb12a7929
children ac2040a5e6ff
comparison
equal deleted inserted replaced
31:cb98f29aa1dc 32:b0d5e752c0c5
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