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annotate 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
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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1 <tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@TOOL_VERSION@">
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2 <description>remove intervals based on overlaps</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements" />
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7 <expand macro="stdio" />
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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8 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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9 bedtools subtract
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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10 $strand
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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11 -a '$inputA'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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12 -b '$inputB'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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13 @OVERLAP@
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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14 $removeIfOverlap
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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15 > '$output'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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16 ]]></command>
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17 <inputs>
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18 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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19 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/>
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20 <expand macro="strand2" />
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21 <expand macro="overlap" />
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22 <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?">
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23 <option value="" selected="true">Don't Remove entire feature on overlap</option>
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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>
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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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>
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26 </param>
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27 </inputs>
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28 <outputs>
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29 <data name="output" format_source="inputA" metadata_source="inputA"/>
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30 </outputs>
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31 <tests>
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32 <test>
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33 <param name="inputA" value="subtractBed1.bed" ftype="bed" />
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34 <param name="inputB" value="subtractBed2.bed" ftype="bed" />
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35 <output name="output" file="subtractBed_result1.bed" ftype="bed" />
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36 </test>
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37 <test>
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38 <param name="inputA" value="subtractBed1.bed" ftype="bed" />
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39 <param name="inputB" value="subtractBed2.bed" ftype="bed" />
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40 <param name="overlap" value="0.80" />
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41 <output name="output" file="subtractBed_result2.bed" ftype="bed" />
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42 </test>
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43 <test>
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44 <param name="inputA" value="subtractBed1.bed" ftype="bed" />
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45 <param name="inputB" value="subtractBed2.bed" ftype="bed" />
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46 <param name="removeIfOverlap" value="-A" />
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47 <output name="output" file="subtractBed_result3.bed" ftype="bed" />
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48 </test>
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49 </tests>
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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50 <help><![CDATA[
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51 **What it does**
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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.
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54
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55 .. image:: $PATH_TO_IMAGES/subtract-glyph.png
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57 @REFERENCES@
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58 ]]></help>
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59 <expand macro="citations" />
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60 </tool>