annotate annotateBed.xml @ 23:13400f3c3ec5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6418f2e58def1a81b3aa7c04cb5dc33decea1a96
author iuc
date Fri, 09 Feb 2018 09:00:06 -0500
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7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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1 <tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
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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="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
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11 bedtools annotate
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12 -i "${inputA}"
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13 #if $names.names_select == 'yes':
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14 -files
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15 #for $bed in $names.beds:
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16 "${bed.input}"
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17 #end for
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18
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19 -names
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20 #for $bed in $names.beds:
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21 "${bed.inputName}"
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22 #end for
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23 #else:
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24 #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
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25 -files "${files}"
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26 #set names = '" "'.join( [ str( $name.display_name ) for $name in $names.beds ] )
607c0576c6ab planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 6692e3a4fa1bf6e9a407735afdbb2454ed32b316
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27 -names "${names}"
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28 #end if
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29 $strand
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30 $counts
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31 $both
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32 > "${output}"
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33 ]]>
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34 </command>
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35 <inputs>
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36 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" />
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37 <!-- Additional files, if the user needs more -->
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38 <conditional name="names">
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39 <param name="names_select" type="select" label="Specify names for each file">
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40 <option value="no" selected="True">No</option>
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41 <option value="yes">Yes</option>
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42 </param>
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43 <when value="yes">
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44 <repeat name="beds" title="Add BED files and names" >
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45 <param name="input" format="bed" type="data" label="BED file" />
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46 <param name="inputName" type="text" label="Name of the file" />
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47 </repeat>
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48 </when>
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49 <when value="no">
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50 <param name="beds" format="bed" multiple="True" type="data" label="BED file" />
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51 </when>
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52 </conditional>
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53 <expand macro="strand2" />
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54 <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue=""
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55 label="Report the count of features followed by the % coverage for each annotation file"
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56 help="Default is to report solely the fraction of -i covered by each file." />
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57 <param name="both" type="boolean" checked="false" truevalue="-both" falsevalue=""
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7308cc546a36 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 19967671ddd4e750f53d71274e5c12325a402811
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58 label="Report the count of features followed by the % coverage for each annotation file"
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59 help="Default is to report solely the fraction of the input file covered by each file." />
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60 </inputs>
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61 <outputs>
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62 <data format="bed" name="output" />
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63 </outputs>
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64 <tests>
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65 <test>
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66 <param name="inputA" value="annotateBed1.bed" ftype="bed" />
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67 <param name="names_select" value="no" />
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68 <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed" />
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69 <output name="output" file="annotateBed_result.bed" ftype="bed" />
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70 </test>
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71 </tests>
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72 <help>
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73 <![CDATA[
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74 **What it does**
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75
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76 bedtools annotate, well, annotates one BED/VCF/GFF file with the coverage and number of overlaps observed from multiple other BED/VCF/GFF 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 ]]>
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80 </help>
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81 <expand macro="citations" />
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82 </tool>