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1 <tool id="bedtools_makewindowsbed" name="MakeWindowsBed" version="0.2.0">
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2 <description></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 bedtools makewindows
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10 #if $type.type_select == 'genome':
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11 -g $type.genome
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12 #else:
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13 -i $type.inputA
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14 #end if
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15 #if $action.action_select == 'windowsize':
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16 -w $action.windowsize
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17 #if $action.step_size.step_size_select == 'yes':
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18 -s $action.step_size.step_size
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19 #end if
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20 #else:
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21 -n $action.number
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22 #end if
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23 $sourcename
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24 > $output
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25 </command>
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26 <inputs>
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27 <conditional name="type">
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28 <param name="type_select" type="select" label="Work with">
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29 <option value="bed" selected="True">Bed File</option>
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30 <option value="genome">Genome File</option>
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31 </param>
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32 <when value="bed">
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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 </when>
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35 <when value="genome">
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36 <expand macro="genome" />
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37 </when>
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38 </conditional>
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39 <conditional name="action">
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40 <param name="action_select" type="select" label="Work with">
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41 <option value="windowsize" selected="True">Set WindowSize</option>
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42 <option value="number">Give Number of Windows</option>
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43 </param>
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44 <when value="windowsize">
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45 <param name="windowsize" type="integer" value="1" label="Divide each input interval (either a chromosome or a BED interval) to fixed-sized windows (i.e. same number of nucleotide in each window)." />
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46 <conditional name="step_size">
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47 <param name="step_size_select" type="select" label="Specify Step size? i.e. how many base pairs to step before creating a new window. Used to create 'sliding' windows. Defaults to window size (non-sliding windows).">
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48 <option value="yes">Yes</option>
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49 <option value="no" selected="True">No</option>
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50 </param>
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51 <when value="yes">
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52 <param name="step_size" type="integer" value="100" label="Specify it" />
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53 </when>
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54 </conditional>
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55 </when>
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56 <when value="number">
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57 <param name="number" type="integer" value="1" label="Divide each input interval (either a chromosome or a BED interval) to fixed number of windows (i.e. same number of windows, with varying window sizes)." />
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58 </when>
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59 </conditional>
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60 <param name="sourcename" type="select" label="ID Naming Options">
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61 <option value="" selected="True">Default</option>
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62 <option value="-i src">use the source interval's name</option>
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63 <option value="-i winnum">use the window number as the ID (e.g. 1,2,3,4...)</option>
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64 <option value="-i srcwinnum">use the source interval's name with the window number.</option>
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65 </param>
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66 </inputs>
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67 <outputs>
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68 <data format_source="inputA" name="output" metadata_source="inputA" label=""/>
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69 </outputs>
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70 <help>
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71
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72 **What it does**
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73
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74 Makes adjacent or sliding windows across a genome or BED file.
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75
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76 @REFERENCES@
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77 </help>
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78 </tool>
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