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annotate randomBed.xml @ 21:b3c147390100 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 3113ecabff4cd259d175b638fd5ff14f0fce6da1
author iuc
date Wed, 10 Jan 2018 19:30:53 -0500
parents a8eabd2838f6
children 4f7a5ccd2ae9
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a8eabd2838f6 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 542ddc9e98cee5cc2a9e4caae945dee4b2c747b8
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1 <tool id="bedtools_randombed" name="RandomBed" version="@WRAPPER_VERSION@.0">
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2 <description>generate random intervals in a genome</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 random
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11 -g @GENOME_FILE@
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12 -l $length
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13 -n $intervals
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14 #if str($seed.seed_choose) == "True":
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15 -seed $seed.seed
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16 #end if
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17 > "$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="input_conditional_genome_file" />
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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_file_opts_selector" value="hist" />
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32 <param name="genome" value="mm9_chr1.len" />
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33 <param name="seed_choose" value="False" />
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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">
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37 <assert_contents>
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38 <has_text_matching expression="chr1" />
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39 <has_n_columns n="6" />
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40 </assert_contents>
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41 </output>
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42 </test>
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43 </tests>
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44 <help>
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45 <![CDATA[
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46 **What it does**
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47
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48 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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49
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50 @REFERENCES@
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51 ]]>
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52 </help>
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53 <expand macro="citations" />
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54 </tool>