Mercurial > repos > iuc > bedtools
view subtractBed.xml @ 27:a33db97b220c draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1ec398a9421f016b852fe59d46961c12321ee5c8
author | iuc |
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date | Tue, 15 May 2018 14:52:10 -0400 |
parents | 95a3b2c25bd1 |
children | 4f7a5ccd2ae9 |
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<tool id="bedtools_subtractbed" name="SubtractBed" version="@WRAPPER_VERSION@.0"> <description>remove intervals based on overlaps</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements" /> <expand macro="stdio" /> <command> <![CDATA[ bedtools subtract $strand -a '$inputA' -b '$inputB' -f $overlap $removeIfOverlap > '$output' ]]> </command> <inputs> <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> <expand macro="strand2" /> <expand macro="overlap" /> <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?"> <option value="" selected="True">Dont Remove entire feature on overlap</option> <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> <option value="-N">Same as -A except when used with -f, the amount is the sum of all features (not any single feature)</option> </param> </inputs> <outputs> <data format_source="inputA" name="output" metadata_source="inputA"/> </outputs> <tests> <test> <param name="inputA" value="subtractBed1.bed" ftype="bed" /> <param name="inputB" value="subtractBed2.bed" ftype="bed" /> <output name="output" file="subtractBed_result1.bed" ftype="bed" /> </test> <test> <param name="inputA" value="subtractBed1.bed" ftype="bed" /> <param name="inputB" value="subtractBed2.bed" ftype="bed" /> <param name="overlap" value="0.80" /> <output name="output" file="subtractBed_result2.bed" ftype="bed" /> </test> <test> <param name="inputA" value="subtractBed1.bed" ftype="bed" /> <param name="inputB" value="subtractBed2.bed" ftype="bed" /> <param name="removeIfOverlap" value="-A" /> <output name="output" file="subtractBed_result3.bed" ftype="bed" /> </test> </tests> <help> <![CDATA[ **What it does** 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. .. image:: $PATH_TO_IMAGES/subtract-glyph.png @REFERENCES@ ]]> </help> <expand macro="citations" /> </tool>