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comparison flankBed.xml @ 34:dde39ba9c031 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author iuc
date Mon, 29 Apr 2019 05:55:48 -0400
parents 4f7a5ccd2ae9
children 3e38c9b3214f
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33:87ee588b3d45 34:dde39ba9c031
1 <tool id="bedtools_flankbed" name="bedtools FlankBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_flankbed" name="bedtools FlankBed" version="@TOOL_VERSION@">
2 <description>create new intervals from the flanks of existing intervals</description> 2 <description>create new intervals from the flanks of existing intervals</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro="requirements" /> 6 <expand macro="requirements" />
7 <expand macro="stdio" /> 7 <expand macro="stdio" />
8 <command> 8 <command><![CDATA[
9 <![CDATA[ 9 flankBed
10 flankBed 10 $pct
11 $pct 11 $strand
12 $strand 12 -g @GENOME_FILE@
13 -g @GENOME_FILE@ 13 -i '$input'
14 -i '$input'
15 14
16 #if $addition.addition_select == 'b': 15 #if $addition.addition_select == 'b':
17 -b $addition.b 16 -b $addition.b
18 #else: 17 #else:
19 -l $addition.l 18 -l $addition.l
20 -r $addition.r 19 -r $addition.r
21 #end if 20 #end if
22 > '$output' 21 > '$output'
23 ]]> 22 ]]></command>
24 </command>
25 <inputs> 23 <inputs>
26 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 24 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
27 <expand macro="input_conditional_genome_file" /> 25 <expand macro="input_conditional_genome_file" />
28 <param name="pct" type="boolean" checked="false" truevalue="-pct" falsevalue="" 26 <param argument="-pct" type="boolean" truevalue="-pct" falsevalue="" checked="false"
29 label="Define -l and -r as a fraction of the feature’s length" 27 label="Define -l and -r as a fraction of the feature’s length"
30 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. (-pct)" /> 28 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
31 <param name="strand" type="boolean" checked="false" truevalue="-s" falsevalue="" 29 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
32 label="Define -l and -r based on strand" 30 label="Define -l and -r based on strand"
33 help="For example. if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate. (-s)" /> 31 help="For example, if used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
34 <expand macro="addition" /> 32 <expand macro="addition" />
35 </inputs> 33 </inputs>
36 <outputs> 34 <outputs>
37 <data metadata_source="input" format_source="input" name="output" /> 35 <data name="output" format_source="input" metadata_source="input" />
38 </outputs> 36 </outputs>
39 <tests> 37 <tests>
40 <test> 38 <test>
41 <param name="input" value="a.bed" ftype="bed" /> 39 <param name="input" value="a.bed" ftype="bed" />
42 <param name="genome_file_opts_selector" value="hist" /> 40 <param name="genome_file_opts_selector" value="hist" />
53 <param name="l" value="2"/> 51 <param name="l" value="2"/>
54 <param name="r" value="3"/> 52 <param name="r" value="3"/>
55 <output name="output" file="flankBed_result2.bed" ftype="bed" /> 53 <output name="output" file="flankBed_result2.bed" ftype="bed" />
56 </test> 54 </test>
57 </tests> 55 </tests>
58 <help> 56 <help><![CDATA[
59 <![CDATA[
60 **What it does** 57 **What it does**
61 58
62 bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval. 59 bedtools flank will optionally create flanking intervals whose size is user-specified fraction of the original interval.
63 60
64 .. image:: $PATH_TO_IMAGES/flank-glyph.png 61 .. image:: $PATH_TO_IMAGES/flank-glyph.png
65 62
66 .. class:: warningmark 63 .. class:: warningmark
67 64
68 In order to prevent creating intervals that violate chromosome boundaries, bedTools flank requires a bedTool genome file defining the length of each chromosome or contig. . This should be a two column tabular file with the chromosome name in the first column and the END coordinate of the chromosome in the second column. 65 In order to prevent creating intervals that violate chromosome boundaries, bedTools flank requires a bedTool genome file defining the length of each chromosome or contig. . This should be a two column tabular file with the chromosome name in the first column and the END coordinate of the chromosome in the second column.
69 66
70 If you need this data for any genome that is at UCSC (http://genome.ucsc.edu), it can be extracted from the Table Browser with the "Get Data: UCSC Main" tool. Set "group" to "All Tables", "table" to "chromInfo", and "output format" to "all fields from selected table". 67 If you need this data for any genome that is at UCSC (http://genome.ucsc.edu), it can be extracted from the Table Browser with the "Get Data: UCSC Main" tool. Set "group" to "All Tables", "table" to "chromInfo", and "output format" to "all fields from selected table".
71
72
73 68
74 @REFERENCES@ 69 @REFERENCES@
75 ]]> 70 ]]></help>
76 </help>
77 <expand macro="citations" /> 71 <expand macro="citations" />
78 </tool> 72 </tool>