annotate annotateBed.xml @ 17:a2d4c30ba2f9 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
author iuc
date Sun, 21 Jun 2015 22:49:46 -0400
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1 <tool id="bedtools_annotatebed" name="AnnotateBed" version="@WRAPPER_VERSION@.0">
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a2d4c30ba2f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 0887009a23d176b21536c9fd8a18c4fecc417d4f
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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 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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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 #set files = '" "'.join( [ str( $file ) for $file in $names.beds ] )
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24 -files "${files}"
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25 #end if
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26 $strand
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27 $counts
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28 $both
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29 > "${output}"
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30 ]]>
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31 </command>
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32 <inputs>
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33 <param format="bed,vcf,gff,gff3" name="inputA" type="data" label="BED/VCF/GFF file" />
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34 <!-- Additional files, if the user needs more -->
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35 <conditional name="names">
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36 <param name="names_select" type="select" label="Specify names for each file">
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37 <option value="no" selected="True">No</option>
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38 <option value="yes">Yes</option>
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39 </param>
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40 <when value="yes">
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41 <repeat name="beds" title="Add BED files and names" >
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42 <param name="input" format="bed" type="data" label="BED file" />
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43 <param name="inputName" type="text" label="Name of the file" />
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44 </repeat>
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45 </when>
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46 <when value="no">
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47 <param name="beds" format="bed" multiple="True" type="data" label="BED file" />
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48 </when>
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49 </conditional>
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50 <expand macro="strand2" />
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51 <param name="counts" type="boolean" checked="false" truevalue="-counts" falsevalue=""
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52 label="Report the count of features followed by the % coverage for each annotation file"
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53 help="Default is to report solely the fraction of -i covered by each file." />
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54 <param name="both" type="boolean" checked="false" truevalue="-both" 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 the input file covered by each file." />
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57 </inputs>
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58 <outputs>
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59 <data format="bed" name="output" />
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="inputA" value="annotateBed1.bed" ftype="bed" />
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64 <param name="names_select" value="no" />
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65 <param name="beds" value="annotateBed2.bed,annotateBed3.bed,annotateBed4.bed" />
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66 <output name="output" file="annotateBed_result.bed" ftype="bed" />
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67 </test>
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68 </tests>
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69 <help>
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70 <![CDATA[
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71 **What it does**
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72
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73 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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75 @REFERENCES@
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76 ]]>
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77 </help>
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78 <expand macro="citations" />
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79 </tool>