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annotate sortBed.xml @ 44:589e7e57fd6d draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 03a91f6c42c75dc36d09505c2e6a2236178e4695
author iuc
date Mon, 20 Feb 2023 21:49:48 +0000
parents 07e8b80f278c
children 64e2edfe7a2c
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589e7e57fd6d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 03a91f6c42c75dc36d09505c2e6a2236178e4695
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1 <tool id="bedtools_sortbed" name="bedtools SortBED" version="@TOOL_VERSION@+galaxy2" profile="@PROFILE@">
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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="bio_tools" />
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <command><![CDATA[
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10 sortBed
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11 -i '$input'
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12 $option
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13 @GENOME_FILE@
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14 > '$output'
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15 ]]></command>
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16 <inputs>
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17 <param name="input" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" 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 <expand macro="input_conditional_genome_file" optional="true" help="Sort according to the chromosomes declared in a genome file" />
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29 </inputs>
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30 <outputs>
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31 <data name="output" format_source="input" metadata_source="input" label="SortBed on ${input.name}"/>
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32 </outputs>
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33 <tests>
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34 <test>
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35 <param name="input" value="sortBed1.bed" ftype="bed" />
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36 <param name="option" value="" />
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37 <output name="output" file="sortBed_result1.bed" ftype="bed" />
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38 </test>
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39 <test>
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40 <param name="input" value="sortBed2.bed" ftype="bed" />
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41 <param name="option" value="" />
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42 <output name="output" file="sortBed_result2.bed" ftype="bed" />
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43 </test>
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44 <test>
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45 <param name="input" value="sortBed2.bed" ftype="bed" />
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46 <param name="option" value="" />
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47 <conditional name="genome_file_opts">
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48 <param name="genome_file_opts_selector" value="hist" />
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49 <param name="genome" value="mm9.len" ftype="bed" />
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50 </conditional>
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51 <output name="output" file="sortBed_result3.bed" ftype="bed" />
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52 </test>
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53 </tests>
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54 <help><![CDATA[
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55 **What it does**
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56
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57 Sorts a feature file by chromosome and other criteria.
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59
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60 .. class:: warningmark
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61
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62 It should be noted that sortBed is merely a convenience utility, as the UNIX sort utility
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63 will sort BED files more quickly while using less memory. For example, UNIX sort will sort a BED file
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64 by chromosome then by start position in the following manner: sort -k 1,1 -k2,2 -n a.bed
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65
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66 @REFERENCES@
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67 ]]></help>
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68 <expand macro="citations" />
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69 </tool>