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annotate slopBed.xml @ 45:a1a923cd89e8 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit d1ee301a39e9830693eedb6ca089456081540f28
author iuc
date Thu, 02 Mar 2023 08:52:08 +0000
parents 07e8b80f278c
children 64e2edfe7a2c
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07e8b80f278c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit db0b91a784ca0c216345bc488d7d488babf1b53f"
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1 <tool id="bedtools_slopbed" name="bedtools SlopBed" version="@TOOL_VERSION@+galaxy1" profile="@PROFILE@">
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2 <description>adjust the size of 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 bedtools slop
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11 $pct
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12 $strand
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13 @GENOME_FILE@
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14 -i '$inputA'
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15 #if $addition.addition_select == 'b':
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16 -b $addition.b
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17 #else:
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18 -l $addition.l
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19 -r $addition.r
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20 #end if
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21 $header
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22 > '$output'
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23 ]]></command>
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24 <inputs>
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25 <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
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26 <expand macro="input_conditional_genome_file" />
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27 <param argument="-pct" type="boolean" truevalue="-pct" falsevalue="" checked="false"
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28 label="Define -l and -r as a fraction of the feature’s length"
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29 help="E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”" />
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30 <param name="strand" argument="-s" type="boolean" truevalue="-s" falsevalue="" checked="false"
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31 label="Define -l and -r based on strand"
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32 help="If used, -l 500 for a negative-stranded feature, it will add 500 bp to the end coordinate" />
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33 <expand macro="addition" />
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34 <expand macro="print_header" />
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35 </inputs>
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36 <outputs>
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37 <data name="output" format="bed" />
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38 </outputs>
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39 <tests>
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40 <test>
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41 <param name="inputA" value="a.bed" ftype="bed" />
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42 <param name="genome_file_opts_selector" value="hist" />
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43 <param name="genome" value="mm9_chr1.len" ftype="bed" />
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44 <param name="addition_select" value="b" />
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45 <param name="b" value="5" />
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46 <output name="output" file="slopBed_result1.bed" ftype="bed" />
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47 </test>
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48 <test>
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49 <param name="inputA" value="a.bed" ftype="bed" />
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50 <param name="genome_file_opts_selector" value="hist" />
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51 <param name="genome" value="mm9_chr1.len" ftype="bed" />
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52 <param name="addition_select" value="lr" />
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53 <param name="l" value="2" />
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54 <param name="r" value="3" />
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55 <output name="output" file="slopBed_result2.bed" ftype="bed" />
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56 </test>
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57 </tests>
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58 <help><![CDATA[
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59 **What it does**
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60
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61 bedtools slop will increase the size of each feature in a feature file by a user-defined number of bases. While something like this could be done with an awk '{OFS="\t" print $1,$2-&lt;slop>,$3+&lt;slop>}', bedtools slop will restrict the resizing to the size of the chromosome (i.e. no start &lt; 0 and no end > chromosome size).
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63 .. image:: $PATH_TO_IMAGES/slop-glyph.png
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64
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65 .. class:: warningmark
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66
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67 In order to prevent the extension of intervals beyond chromosome boundaries, bedtools slop requires a genome file defining the length of each chromosome or contig.
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68
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69 @REFERENCES@
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70 ]]></help>
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71 <expand macro="citations" />
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72 </tool>