Mercurial > repos > iuc > bedtools
annotate subtractBed.xml @ 26:95a3b2c25bd1 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
| author | iuc |
|---|---|
| date | Thu, 26 Apr 2018 17:02:46 -0400 |
| parents | 7308cc546a36 |
| children | 4f7a5ccd2ae9 |
| rev | line source |
|---|---|
| 0 | 1 <tool id="bedtools_subtractbed" name="SubtractBed" version="@WRAPPER_VERSION@.0"> |
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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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1
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changeset
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2 <description>remove intervals based on overlaps</description> |
| 0 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 1 | 9 <![CDATA[ |
| 0 | 10 bedtools subtract |
| 11 $strand | |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
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12 -a '$inputA' |
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7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
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13 -b '$inputB' |
| 0 | 14 -f $overlap |
| 15 $removeIfOverlap | |
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11
7308cc546a36
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
4
diff
changeset
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16 > '$output' |
| 1 | 17 ]]> |
| 0 | 18 </command> |
| 19 <inputs> | |
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95a3b2c25bd1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents:
11
diff
changeset
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20 <param format="@STD_BEDTOOLS_INPUTS@" name="inputA" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
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95a3b2c25bd1
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents:
11
diff
changeset
|
21 <param format="@STD_BEDTOOLS_INPUTS@" name="inputB" type="data" label="@STD_BEDTOOLS_INPUT_LABEL@ file"/> |
| 0 | 22 <expand macro="strand2" /> |
| 23 <expand macro="overlap" /> | |
| 24 <param name="removeIfOverlap" type="select" label="Calculation based on strandedness?"> | |
| 25 <option value="" selected="True">Dont Remove entire feature on overlap</option> | |
| 1 | 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> |
| 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> | |
| 0 | 28 </param> |
| 29 </inputs> | |
| 30 <outputs> | |
| 1 | 31 <data format_source="inputA" name="output" metadata_source="inputA"/> |
| 0 | 32 </outputs> |
| 1 | 33 <tests> |
| 34 <test> | |
| 35 <param name="inputA" value="subtractBed1.bed" ftype="bed" /> | |
| 36 <param name="inputB" value="subtractBed2.bed" ftype="bed" /> | |
| 37 <output name="output" file="subtractBed_result1.bed" ftype="bed" /> | |
| 38 </test> | |
| 39 <test> | |
| 40 <param name="inputA" value="subtractBed1.bed" ftype="bed" /> | |
| 41 <param name="inputB" value="subtractBed2.bed" ftype="bed" /> | |
| 42 <param name="overlap" value="0.80" /> | |
| 43 <output name="output" file="subtractBed_result2.bed" ftype="bed" /> | |
| 44 </test> | |
| 45 <test> | |
| 46 <param name="inputA" value="subtractBed1.bed" ftype="bed" /> | |
| 47 <param name="inputB" value="subtractBed2.bed" ftype="bed" /> | |
| 48 <param name="removeIfOverlap" value="-A" /> | |
| 49 <output name="output" file="subtractBed_result3.bed" ftype="bed" /> | |
| 50 </test> | |
| 51 </tests> | |
| 0 | 52 <help> |
| 1 | 53 <![CDATA[ |
| 0 | 54 **What it does** |
| 55 | |
| 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. | |
| 57 | |
| 58 .. image:: $PATH_TO_IMAGES/subtract-glyph.png | |
| 59 | |
| 60 @REFERENCES@ | |
| 1 | 61 ]]> |
| 0 | 62 </help> |
| 63 <expand macro="citations" /> | |
| 64 </tool> |