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1 <tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.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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4
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9 <![CDATA[
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10 bedtools random
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11 -g $genome
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12 -l $length
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13 -n $intervals
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6
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14 #if str($seed.seed_choose) == "True":
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15 -seed $seed.seed
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16 #end if
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4
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17 > "$output"
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18 ]]>
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19 </command>
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20 <inputs>
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21 <expand macro="genome" />
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22 <param name="length" type="integer" value="100" label="The length of the intervals to generate" help="(-l)" />
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23 <param name="intervals" type="integer" value="1000000" label="The number of intervals to generate" help="(-n)" />
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24 <expand macro="seed" />
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25 </inputs>
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26 <outputs>
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27 <data format="bed" name="output" />
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28 </outputs>
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29 <tests>
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30 <test>
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31 <param name="genome" value="mm9_chr1.len" />
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32 <param name="seed_choose" value="True" />
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33 <param name="seed" value="1" />
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34 <param name="length" value="5" />
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35 <param name="intervals" value="3" />
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36 <output name="output" file="randomBed_result1.bed" ftype="bed" />
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37 </test>
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38 <test>
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39 <param name="genome" value="mm9_chr1.len" />
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40 <param name="seed_choose" value="False" />
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41 <param name="length" value="5" />
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42 <param name="intervals" value="3" />
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43 <output name="output">
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44 <assert_contents>
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45 <has_text_matching expression="chr1" />
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46 <has_n_columns n="6" />
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47 </assert_contents>
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48 </output>
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49 </test>
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50 </tests>
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51 <help>
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52 <![CDATA[
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53 **What it does**
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54
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55 bedtools random will generate a random set of intervals in BED6 format. One can specify both the number (-n) and the size (-l) of the intervals that should be generated.
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56
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57 @REFERENCES@
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4
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58 ]]>
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59 </help>
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1
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60 <expand macro="citations" />
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61 </tool>
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