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annotate annotateBed.xml @ 64:f6c88d2e9ae5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 73ebd55430874a3c1483b6dd6cce0482175482f9
author iuc
date Fri, 21 Feb 2025 21:38:34 +0000
parents 539958feb49c
children
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1d0a0d6a78b1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 1e25e8d0bd1ebeb2b94c4bbdff222e56defc1fc2"
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1 <tool id="bedtools_annotatebed" name="bedtools AnnotateBed" version="@TOOL_VERSION@" profile="@PROFILE@">
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2 <description>annotate coverage of features from multiple files</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 annotate
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11 -i '${inputA}'
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12 #if $names.names_select == 'yes':
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13 -files
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14 #for $bed in $names.beds:
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15 '${bed.input}'
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16 #end for
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17
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18 -names
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19 #for $bed in $names.beds:
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20 '${bed.inputName}'
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21 #end for
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22 #else:
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23 -files
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24 #for $bed in $names.beds:
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25 '$bed'
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26 #end for
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27 -names
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28 #for $bed in $names.beds:
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29 '${bed.display_name}'
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30 #end for
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31 #end if
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32 $strand
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33 $counts
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34 $both
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35 > '${output}'
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36 ]]></command>
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37 <inputs>
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38 <param name="inputA" argument="-i" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
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39 <conditional name="names">
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40 <param name="names_select" type="select" label="Specify names for each file">
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41 <option value="no" selected="true">No</option>
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42 <option value="yes">Yes</option>
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43 </param>
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44 <when value="yes">
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45 <repeat name="beds" title="Add BED files and names" >
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46 <param name="input" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
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47 <param name="inputName" type="text" label="Name of the file" />
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48 </repeat>
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49 </when>
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50 <when value="no">
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51 <param name="beds" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
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52 </when>
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53 </conditional>
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54 <expand macro="strand2" />
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55 <param argument="-counts" type="boolean" truevalue="-counts" falsevalue="" checked="false"
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56 label="Report the count of features followed by the % coverage for each annotation file"
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57 help="Default is to report solely the fraction of -i covered by each file" />
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58 <param argument="-both" type="boolean" truevalue="-both" falsevalue="" checked="false"
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59 label="Report the count of features followed by the % coverage for each annotation file"
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60 help="Default is to report solely the fraction of the input file covered by each file" />
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61 </inputs>
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62 <outputs>
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63 <data name="output" format="bed" />
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64 </outputs>
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65 <tests>
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66 <test>
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67 <param name="inputA" value="annotateBed1.bed" ftype="bed" />
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68 <param name="names|names_select" value="no" />
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69 <param name="names|beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed"/>
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70 <output name="output" file="annotateBed_result.bed" ftype="bed" />
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71 </test>
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72 </tests>
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73 <help><![CDATA[
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74 **What it does**
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75
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76 bedtools annotate, well, annotates one @STD_BEDTOOLS_INPUT_LABEL@ file with the coverage and number of overlaps observed from multiple other @STD_BEDTOOLS_INPUT_LABEL@ files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.
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78 @REFERENCES@
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79 ]]></help>
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80 <expand macro="citations" />
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81 </tool>