Mercurial > repos > iuc > bedtools
annotate subtractBed.xml @ 43:07e8b80f278c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
author | iuc |
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date | Fri, 01 Apr 2022 19:02:51 +0000 |
parents | 7ab85ac5f64b |
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rev | line source |
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3e38c9b3214f
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
iuc
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1 <tool id="bedtools_subtractbed" name="bedtools SubtractBed" version="@TOOL_VERSION@" profile="@PROFILE@"> |
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607c0576c6ab
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
iuc
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2 <description>remove intervals based on overlaps</description> |
0 | 3 <macros> |
4 <import>macros.xml</import> | |
5 </macros> | |
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7ab85ac5f64b
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 500a03281ea704abc7a16d9af63d67dbdcc5cd0b"
iuc
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6 <expand macro="bio_tools" /> |
0 | 7 <expand macro="requirements" /> |
8 <expand macro="stdio" /> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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9 <command><![CDATA[ |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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10 bedtools subtract |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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11 $strand |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
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12 -a '$inputA' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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13 -b '$inputB' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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14 @OVERLAP@ |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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15 $removeIfOverlap |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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16 > '$output' |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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17 ]]></command> |
0 | 18 <inputs> |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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19 <param name="inputA" argument="-a" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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20 <param name="inputB" argument="-b" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
0 | 21 <expand macro="strand2" /> |
22 <expand macro="overlap" /> | |
23 <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?"> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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24 <option value="" selected="true">Don't Remove entire feature on overlap</option> |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
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changeset
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25 <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> |
dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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26 <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> |
0 | 27 </param> |
28 </inputs> | |
29 <outputs> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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30 <data name="output" format_source="inputA" metadata_source="inputA"/> |
0 | 31 </outputs> |
1 | 32 <tests> |
33 <test> | |
34 <param name="inputA" value="subtractBed1.bed" ftype="bed" /> | |
35 <param name="inputB" value="subtractBed2.bed" ftype="bed" /> | |
36 <output name="output" file="subtractBed_result1.bed" ftype="bed" /> | |
37 </test> | |
38 <test> | |
39 <param name="inputA" value="subtractBed1.bed" ftype="bed" /> | |
40 <param name="inputB" value="subtractBed2.bed" ftype="bed" /> | |
41 <param name="overlap" value="0.80" /> | |
42 <output name="output" file="subtractBed_result2.bed" ftype="bed" /> | |
43 </test> | |
44 <test> | |
45 <param name="inputA" value="subtractBed1.bed" ftype="bed" /> | |
46 <param name="inputB" value="subtractBed2.bed" ftype="bed" /> | |
47 <param name="removeIfOverlap" value="-A" /> | |
48 <output name="output" file="subtractBed_result3.bed" ftype="bed" /> | |
49 </test> | |
50 </tests> | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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51 <help><![CDATA[ |
0 | 52 **What it does** |
53 | |
54 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. | |
55 | |
56 .. image:: $PATH_TO_IMAGES/subtract-glyph.png | |
57 | |
58 @REFERENCES@ | |
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dde39ba9c031
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
iuc
parents:
32
diff
changeset
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59 ]]></help> |
0 | 60 <expand macro="citations" /> |
61 </tool> |