Mercurial > repos > iuc > bedtools
annotate sortBed.xml @ 17:a2d4c30ba2f9 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
| author | iuc |
|---|---|
| date | Sun, 21 Jun 2015 22:49:46 -0400 |
| parents | 0d3aa592ce27 |
| children | c0fbce5dc84a |
| rev | line source |
|---|---|
|
17
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
|
1 <tool id="bedtools_sortbed" name="SortBED" version="@WRAPPER_VERSION@.0"> |
|
a2d4c30ba2f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
iuc
parents:
8
diff
changeset
|
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[ | |
| 10 sortBed | |
| 11 -i $input | |
| 12 $option | |
| 13 > $output | |
| 14 ]]> | |
| 15 </command> | |
| 16 <inputs> | |
| 17 <param format="bed" name="input" type="data" label="Sort the following BED file"/> | |
| 18 <param name="option" type="select" label="Sort by"> | |
| 19 <!-- sort -k 1,1 -k2,2 -n a.bed --> | |
| 20 <option value="">chromosome, then by start position (asc)</option> | |
| 21 <option value="-sizeA">feature size in ascending order.</option> | |
| 22 <option value="-sizeD">feature size in descending order.</option> | |
| 23 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option> | |
| 24 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option> | |
| 25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option> | |
| 26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option> | |
| 27 </param> | |
| 28 </inputs> | |
| 29 <outputs> | |
| 30 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/> | |
| 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> |