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annotate randomBed.xml @ 56:7a06bb42dbb1 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 07:45:56 +0000
parents df28283b3778
children 1d0a0d6a78b1
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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1 <tool id="bedtools_randombed" name="bedtools RandomBed" version="@TOOL_VERSION@">
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2 <description>generate random intervals in a genome</description>
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7a06bb42dbb1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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3 <expand macro="bio_tools" />
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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9 <command><![CDATA[
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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10 bedtools random
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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11 -g @GENOME_FILE@
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12 -l $length
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13 -n $intervals
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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14 #if str($seed.seed_choose) == "True":
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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15 -seed $seed.seed
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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16 #end if
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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17 > '$output'
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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18 ]]></command>
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19 <inputs>
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20 <expand macro="input_conditional_genome_file" />
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21 <param name="length" argument="-l" type="integer" value="100" label="The length of the intervals to generate" />
df28283b3778 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95
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22 <param name="intervals" argument="-n" type="integer" value="1000000" label="The number of intervals to generate" />
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23 <expand macro="seed" />
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24 </inputs>
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25 <outputs>
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26 <data name="output" format="bed" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="genome_file_opts_selector" value="hist" />
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31 <param name="genome" value="mm9_chr1.len" />
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32 <param name="seed_choose" value="False" />
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33 <param name="length" value="5" />
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34 <param name="intervals" value="3" />
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35 <output name="output">
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36 <assert_contents>
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37 <has_text_matching expression="chr1" />
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38 <has_n_columns n="6" />
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39 </assert_contents>
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40 </output>
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41 </test>
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42 </tests>
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43 <help><![CDATA[
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44 **What it does**
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46 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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48 @REFERENCES@
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49 ]]></help>
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50 <expand macro="citations" />
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51 </tool>