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comparison overlapBed.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_overlapbed" name="bedtools OverlapBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_overlapbed" name="bedtools OverlapBed" version="@TOOL_VERSION@">
2 <description>computes the amount of overlap from two intervals</description> 2 <description>computes the amount of overlap from two 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 overlap
10 bedtools overlap 10 -i '$input'
11 -i '$input' 11 -cols $cols
12 -cols $cols 12 > '$output'
13 > '$output' 13 ]]></command>
14 ]]>
15 </command>
16 <inputs> 14 <inputs>
17 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 15 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
18 <param name="cols" type="data_column" multiple="True" data_ref="input" 16 <param name="cols" type="data_column" data_ref="input" multiple="true"
19 label="Specify the columns for the starts and ends of the features for which you’d like to compute the overlap/distance" 17 label="Specify the columns for the starts and ends of the features for which you’d like to compute the overlap/distance"
20 help="The columns must be listed in the following order: start1,end1,start2,end2" /> 18 help="The columns must be listed in the following order: start1,end1,start2,end2" />
21 </inputs> 19 </inputs>
22 <outputs> 20 <outputs>
23 <data format_source="input" name="output" metadata_source="input" label="Overlap of ${input.name}"/> 21 <data name="output" format_source="input" metadata_source="input" label="Overlap of ${input.name}"/>
24 </outputs> 22 </outputs>
25 <tests> 23 <tests>
26 <test> 24 <test>
27 <param name="input" value="windowBed_result1.bed" ftype="bed" /> 25 <param name="input" value="windowBed_result1.bed" ftype="bed" />
28 <param name="cols" value="2,3,5,6" /> 26 <param name="cols" value="2,3,5,6" />
29 <output name="output" file="overlapBed_result1.bed" ftype="bed" /> 27 <output name="output" file="overlapBed_result1.bed" ftype="bed" />
30 </test> 28 </test>
31 </tests> 29 </tests>
32 <help> 30 <help><![CDATA[
33 <![CDATA[
34 **What it does** 31 **What it does**
35 32
36 overlap computes the amount of overlap (in the case of positive values) or distance (in the case of negative values) between feature coordinates occurring on the same input line and reports the result at the end of the same line. In this way, it is a useful method for computing custom overlap scores from the output of other BEDTools. 33 overlap computes the amount of overlap (in the case of positive values) or distance (in the case of negative values) between feature coordinates occurring on the same input line and reports the result at the end of the same line. In this way, it is a useful method for computing custom overlap scores from the output of other BEDTools.
37 34
38 @REFERENCES@ 35 @REFERENCES@
39 ]]> 36 ]]></help>
40 </help>
41 <expand macro="citations" /> 37 <expand macro="citations" />
42 </tool> 38 </tool>