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1 <tool id="bedExtendRanges" name="bedExtendRanges">
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2 <description> Extend length of entries in bed 6+. </description>
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3 <requirements>
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4 <requirement type="package" version="1.0">bedExtendRanges</requirement>
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5 </requirements>
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6 <command>
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7 ## Set genome assembly
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8
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9 #set $Genome = str( $genome_cond.genome )
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10 #if str( $genome_cond ) == 'OTHER':
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11 #set $Genome = str( $genome_cond.genome_other )
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12 #end if
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13
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14 bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu $Genome $length $input 2> /dev/null > $output
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15 </command>
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16 <inputs>
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17 <param name="input" type="data" format="bed" label="Input"/>
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18 <conditional name="genome_cond">
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19 <param name="genome" type="select" label="Genome Assembly (-g)">
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20 <option value="hg19">Human (Homo sapiens): hg19</option>
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21 <option value="hg18">Human (Homo sapiens): hg18</option>
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22 <option value="mm10">Mouse (Mus musculus): mm10</option>
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23 <option value="mm9">Mouse (Mus musculus): mm9</option>
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24 <option value="ce10">C. elegans: ce10</option>
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25 <option value="ce6">C. elegans: ce6</option>
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26 <option value="dm3">D. melanogaster: dm3</option>
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27 <option value="OTHER">Other</option>
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28 </param>
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29 <when value="OTHER">
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30 <param name="genome_other" type="text" label="Other genome assemly"/>
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31 </when>
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32 <when value="hg19" type="text" />
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33 <when value="hg18" type="text" />
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34 <when value="mm10" type="text" />
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35 <when value="mm9" type="text" />
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36 <when value="ce10" type="text" />
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37 <when value="ce6" type="text" />
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38 <when value="dm3" type="text" />
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39 </conditional>
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40 <param name="length" type="integer" value="0" label="Length extension (base-pairs)" />
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41
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42 </inputs>
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43
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44 <outputs>
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45 <data format="input" name="output"/>
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46 </outputs>
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47
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48 <tests>
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49 <test>
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50 <param name="input" value="2.bed" />
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51 <param name="genome" value="hg19" />
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52 <param name="length" value="5000" />
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53 <output name="output" file="4.bed" />
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54 </test>
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55 </tests>
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56
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57 <help>
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58
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59 **What it does**
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60
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61 bedExtendRanges_ - extend length of entries in bed 6+ data to be at least the given length,
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62 taking strand directionality into account.
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63
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64 .. _bedExtendRanges: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bedExtendRanges
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65
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66 **Usage**
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67
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68 bedExtendRanges database length files(s)
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69
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70 **Example**
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71
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72 * bedExtendRanges -user=genome -host=genome-mysql.cse.ucsc.edu hg18 250 stdin
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73
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74 will transform:
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75 chr1 500 525 . 100 +
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76 chr1 1000 1025 . 100 -
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77 to:
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78 chr1 500 750 . 100 +
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79 chr1 775 1025 . 100 -
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80
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81 </help>
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82 </tool>
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