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1 <tool id="bedClip" name="bedClip">
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2 <description> Remove lines from bed file that refer to off-chromosome places.</description>
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3 <requirements>
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4 <requirement type="package" version="1.0">fetchChromSizes</requirement>
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5 <requirement type="package" version="1.0">bedClip</requirement>
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6 </requirements>
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7 <command interpreter="bash">
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8 ## Set genome assembly
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9
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10 #set $Genome = str( $genome_cond.genome )
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11 #if str( $genome_cond ) == 'OTHER':
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12 #set $Genome = str( $genome_cond.genome_other )
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13 #end if
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14
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15 bedClip.sh $input $Genome $output
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16 </command>
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17 <inputs>
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18 <param name="input" type="data" format="bed" label="Input"/>
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19 <conditional name="genome_cond">
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20 <param name="genome" type="select" label="Genome Assembly">
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21 <option value="hg19">Human (Homo sapiens): hg19</option>
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22 <option value="hg18">Human (Homo sapiens): hg18</option>
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23 <option value="mm10">Mouse (Mus musculus): mm10</option>
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24 <option value="mm9">Mouse (Mus musculus): mm9</option>
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25 <option value="ce10">C. elegans: ce10</option>
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26 <option value="ce6">C. elegans: ce6</option>
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27 <option value="dm3">D. melanogaster: dm3</option>
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28 <option value="OTHER">Other</option>
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29 </param>
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30 <when value="OTHER">
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31 <param name="genome_other" type="text" label="Other genome assemly"/>
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32 </when>
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33 <when value="hg19" type="text" />
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34 <when value="hg18" type="text" />
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35 <when value="mm10" type="text" />
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36 <when value="mm9" type="text" />
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37 <when value="ce10" type="text" />
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38 <when value="ce6" type="text" />
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39 <when value="dm3" type="text" />
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40 </conditional>
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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="3.bed" />
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51 <param name="genome" value="hg19" />
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52 <output name="output" file="1.bed" />
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53 </test>
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54 </tests>
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55
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56 <help>
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57 **What it does**
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58 bedClip - Remove lines from bed file that refer to off-chromosome places.
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59
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60 **Usage**
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61
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62 bedClip input.bed chrom.sizes output.bed
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63
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64 </help>
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65 </tool>
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