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comparison subtractBed.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_subtractbed" name="bedtools SubtractBed" version="@WRAPPER_VERSION@"> 1 <tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@TOOL_VERSION@">
2 <description>remove intervals based on overlaps</description> 2 <description>remove intervals based on overlaps</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 subtract
10 bedtools subtract 10 $strand
11 $strand 11 -a '$inputA'
12 -a '$inputA' 12 -b '$inputB'
13 -b '$inputB' 13 @OVERLAP@
14 -f $overlap 14 $removeIfOverlap
15 $removeIfOverlap 15 > '$output'
16 > '$output' 16 ]]></command>
17 ]]>
18 </command>
19 <inputs> 17 <inputs>
20 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 18 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
21 <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> 19 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
22 <expand macro="strand2" /> 20 <expand macro="strand2" />
23 <expand macro="overlap" /> 21 <expand macro="overlap" />
24 <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?"> 22 <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?">
25 <option value="" selected="True">Dont Remove entire feature on overlap</option> 23 <option value="" selected="true">Don't Remove entire feature on overlap</option>
26 <option value="-A">Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed</option> 24 <option value="-A">Remove entire feature if any overlap. That is, by default, only subtract the portion of A that overlaps B. Here, if any overlap is found (or -f amount), the entire feature is removed (-A)</option>
27 <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature)</option> 25 <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature) (-N)</option>
28 </param> 26 </param>
29 </inputs> 27 </inputs>
30 <outputs> 28 <outputs>
31 <data format_source="inputA" name="output" metadata_source="inputA"/> 29 <data name="output" format_source="inputA" metadata_source="inputA"/>
32 </outputs> 30 </outputs>
33 <tests> 31 <tests>
34 <test> 32 <test>
35 <param name="inputA" value="subtractBed1.bed" ftype="bed" /> 33 <param name="inputA" value="subtractBed1.bed" ftype="bed" />
36 <param name="inputB" value="subtractBed2.bed" ftype="bed" /> 34 <param name="inputB" value="subtractBed2.bed" ftype="bed" />
47 <param name="inputB" value="subtractBed2.bed" ftype="bed" /> 45 <param name="inputB" value="subtractBed2.bed" ftype="bed" />
48 <param name="removeIfOverlap" value="-A" /> 46 <param name="removeIfOverlap" value="-A" />
49 <output name="output" file="subtractBed_result3.bed" ftype="bed" /> 47 <output name="output" file="subtractBed_result3.bed" ftype="bed" />
50 </test> 48 </test>
51 </tests> 49 </tests>
52 <help> 50 <help><![CDATA[
53 <![CDATA[
54 **What it does** 51 **What it does**
55 52
56 bedtools subtract searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported. 53 bedtools subtract searches for features in B that overlap A. If an overlapping feature is found in B, the overlapping portion is removed from A and the remaining portion of A is reported. If a feature in B overlaps all of a feature in A, the A feature will not be reported.
57 54
58 .. image:: $PATH_TO_IMAGES/subtract-glyph.png 55 .. image:: $PATH_TO_IMAGES/subtract-glyph.png
59 56
60 @REFERENCES@ 57 @REFERENCES@
61 ]]> 58 ]]></help>
62 </help>
63 <expand macro="citations" /> 59 <expand macro="citations" />
64 </tool> 60 </tool>