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annotate sortBed.xml @ 29:6bb3cd018203 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 69394918e7a50dad3ae578e932cbac27b96e0d3b
author iuc
date Tue, 24 Jul 2018 11:49:55 -0400
parents 95a3b2c25bd1
children 4f7a5ccd2ae9
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607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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1 <tool id="bedtools_sortbed" name="SortBED" version="@WRAPPER_VERSION@.0">
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2 <description>order the intervals</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 <![CDATA[
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10 sortBed
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11 -i '$input'
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12 $option
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13 > '$output'
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14 ]]>
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15 </command>
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16 <inputs>
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17 <param format="@STD_BEDTOOLS_INPUTS@" name="input" type="data" label="Sort the following @STD_BEDTOOLS_INPUT_LABEL@ file"/>
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18 <param name="option" type="select" label="Sort by">
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19 <!-- sort -k 1,1 -k2,2 -n a.bed -->
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20 <option value="">chromosome, then by start position (asc)</option>
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21 <option value="-sizeA">feature size in ascending order.</option>
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22 <option value="-sizeD">feature size in descending order.</option>
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23 <option value="-chrThenSizeA">chromosome, then by feature size (asc).</option>
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24 <option value="-chrThenSizeD">chromosome, then by feature size (desc).</option>
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25 <option value="-chrThenScoreA">chromosome, then by score (asc).</option>
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26 <option value="-chrThenScoreD">chromosome, then by score (desc).</option>
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27 </param>
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28 </inputs>
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29 <outputs>
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30 <data format_source="input" name="output" metadata_source="input" label="SortBed on ${input.name}"/>
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31 </outputs>
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32 <tests>
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33 <test>
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34 <param name="input" value="sortBed1.bed" ftype="bed" />
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35 <param name="option" value="" />
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36 <output name="output" file="sortBed_result1.bed" ftype="bed" />
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37 </test>
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38 </tests>
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39 <help>
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40 <![CDATA[
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41 **What it does**
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42
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43 Sorts a feature file by chromosome and other criteria.
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44
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45
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46 .. class:: warningmark
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47
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48 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility
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49 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
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50 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed
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51
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52 @REFERENCES@
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53 ]]>
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54 </help>
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55 <expand macro="citations" />
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56 </tool>