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comparison slopBed.xml @ 50:df28283b3778 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 05:54:22 -0400
parents 2f457890d8c8
children 7a06bb42dbb1
comparison
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49:5074e81a5ce1 50:df28283b3778
1 <tool id="bedtools_slopbed" name="bedtools SlopBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@">
2 <description>adjust the size of intervals</description> 2 <description>adjust the size of 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 bedtools slop
10 bedtools slop 10 $pct
11 $pct 11 $strand
12 $strand 12 -g @GENOME_FILE@
13 -g @GENOME_FILE@ 13 -i '$inputA'
14 -i '$inputA' 14 #if $addition.addition_select == 'b':
15 #if $addition.addition_select == 'b': 15 -b $addition.b
16 -b $addition.b 16 #else:
17 #else: 17 -l $addition.l
18 -l $addition.l 18 -r $addition.r
19 -r $addition.r 19 #end if
20 #end if 20 $header
21 $header 21 > '$output'
22 > '$output' 22 ]]></command>
23 ]]>
24 </command>
25 <inputs> 23 <inputs>
26 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 24 <param name="inputA" 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”" /> 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="If used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" /> 31 help="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 <expand macro="print_header" /> 33 <expand macro="print_header" />
36 </inputs> 34 </inputs>
37 <outputs> 35 <outputs>
38 <data format="bed" name="output"/> 36 <data name="output" format="bed" />
39 </outputs> 37 </outputs>
40 <tests> 38 <tests>
41 <test> 39 <test>
42 <param name="inputA" value="a.bed" ftype="bed" /> 40 <param name="inputA" value="a.bed" ftype="bed" />
43 <param name="genome_file_opts_selector" value="hist" /> 41 <param name="genome_file_opts_selector" value="hist" />
54 <param name="l" value="2" /> 52 <param name="l" value="2" />
55 <param name="r" value="3" /> 53 <param name="r" value="3" />
56 <output name="output" file="slopBed_result2.bed" ftype="bed" /> 54 <output name="output" file="slopBed_result2.bed" ftype="bed" />
57 </test> 55 </test>
58 </tests> 56 </tests>
59 <help> 57 <help><![CDATA[
60 <![CDATA[
61 **What it does** 58 **What it does**
62 59
63 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-&lt;slop>,$3+&lt;slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start &lt; 0 and no end > chromosome size). 60 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-&lt;slop>,$3+&lt;slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start &lt; 0 and no end > chromosome size).
64 61
65 .. image:: $PATH_TO_IMAGES/slop-glyph.png 62 .. image:: $PATH_TO_IMAGES/slop-glyph.png
66 63
67 .. class:: warningmark 64 .. class:: warningmark
68 65
69 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig. 66 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig.
67
70 @REFERENCES@ 68 @REFERENCES@
71 ]]> 69 ]]></help>
72 </help>
73 <expand macro="citations" /> 70 <expand macro="citations" />
74 </tool> 71 </tool>