Mercurial > repos > iuc > bedtools
annotate sortBed.xml @ 48:2f457890d8c8 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
| author | iuc |
|---|---|
| date | Tue, 11 Dec 2018 13:59:34 -0500 |
| parents | d279800f4ff9 |
| children | df28283b3778 |
| rev | line source |
|---|---|
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48
2f457890d8c8
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit fc3616bd1463afef9681cd7c431ac29f79e37e74
iuc
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42
diff
changeset
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1 <tool id="bedtools_sortbed" name="bedtools SortBED" version="@WRAPPER_VERSION@"> |
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17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
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8
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changeset
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2 <description>order the intervals</description> |
| 8 | 3 <macros> |
| 4 <import>macros.xml</import> | |
| 5 </macros> | |
| 6 <expand macro="requirements" /> | |
| 7 <expand macro="stdio" /> | |
| 8 <command> | |
| 9 <![CDATA[ | |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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10 sortBed |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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11 -i '$input' |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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12 $option |
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c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
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13 > '$output' |
| 8 | 14 ]]> |
| 15 </command> | |
| 16 <inputs> | |
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42
d279800f4ff9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b75b9e79cf3186a22dc2e1e9d27c1a080b891b59
iuc
parents:
26
diff
changeset
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17 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file"/> |
| 8 | 18 <param name="option" type="select" label="Sort by"> |
| 19 <!-- sort -k 1,1 -k2,2 -n a.bed --> | |
| 20 <option value="">chromosome, then by start position (asc)</option> | |
| 21 <option value="-sizeA">feature size in ascending order.</option> | |
| 22 <option value="-sizeD">feature size in descending order.</option> | |
| 23 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option> | |
| 24 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option> | |
| 25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option> | |
| 26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option> | |
| 27 </param> | |
| 28 </inputs> | |
| 29 <outputs> | |
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26
c0fbce5dc84a
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
iuc
parents:
17
diff
changeset
|
30 <data format_source="input" name="output" metadata_source="input" label="SortBed on ${input.name}"/> |
| 8 | 31 </outputs> |
| 32 <tests> | |
| 33 <test> | |
| 34 <param name="input" value="sortBed1.bed" ftype="bed" /> | |
| 35 <param name="option" value="" /> | |
| 36 <output name="output" file="sortBed_result1.bed" ftype="bed" /> | |
| 37 </test> | |
| 38 </tests> | |
| 39 <help> | |
| 40 <![CDATA[ | |
| 41 **What it does** | |
| 42 | |
| 43 Sorts a feature file by chromosome and other criteria. | |
| 44 | |
| 45 | |
| 46 .. class:: warningmark | |
| 47 | |
| 48 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility | |
| 49 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file | |
| 50 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed | |
| 51 | |
| 52 @REFERENCES@ | |
| 53 ]]> | |
| 54 </help> | |
| 55 <expand macro="citations" /> | |
| 56 </tool> |