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1 <tool id="bedtools_sortbed" name="Sort BED files" version="0.2.0">
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2 <description></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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8 <command>
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9 sortBed -i $input $option > $output
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10 </command>
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11 <inputs>
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12 <param format="bed" name="input" type="data" label="Sort the following BED file"/>
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13 <param name="option" type="select" label="Sort by">
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14 <!-- sort -k 1,1 -k2,2 -n a.bed -->
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15 <option value="">chromosome, then by start position (asc)</option>
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16 <option value="-sizeA">feature size in ascending order.</option>
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17 <option value="-sizeD">feature size in descending order.</option>
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18 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
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19 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
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20 <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
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21 <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
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22 </param>
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23 </inputs>
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24
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25 <outputs>
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26 <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
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27 </outputs>
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28
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29 <help>
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30
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31 **What it does**
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32
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33 Sorts a feature file by chromosome and other criteria.
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34
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35
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36 .. class:: warningmark
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37
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38 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility
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39 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
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40 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed
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41
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42 @REFERENCES@
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43
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44 </help>
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45 </tool>
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