Mercurial > repos > iuc > bedtools
comparison subtractBed.xml @ 34:dde39ba9c031 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
author | iuc |
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date | Mon, 29 Apr 2019 05:55:48 -0400 |
parents | 4f7a5ccd2ae9 |
children | 3e38c9b3214f |
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33:87ee588b3d45 | 34:dde39ba9c031 |
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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> |