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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
author devteam
date Mon, 09 Nov 2015 12:33:58 -0500
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ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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1 <tool id="vcfrandomsample" name="VCFrandomSample:" version="0.0.3">
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2 <description>Randomly sample sites from VCF dataset</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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6 <expand macro="requirements"></expand>
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7 <expand macro="stdio" />
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8 <command>
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9
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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10 #if $adv_options.adv_options_selector == True:
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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11 vcfrandomsample -s "${adv_options.scale_by}" -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}"
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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12 #else:
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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13 vcfrandomsample -p ${random_seed} -r ${rate} "${vcf_input}" > "${out_file1}"
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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14 #end if
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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15 </command>
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16 <inputs>
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17 <param format="vcf" name="vcf_input" type="data" label="Select random sites from"/>
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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18 <param name="rate" type="float" value="0.1" label="base sampling probability per locus" help="-r, --rate"/>
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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19 <param name="random_seed" type="integer" value="17823618326" label="use this random seed" help="-p, --random-seed; use this to make results reproducible" />
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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20 <conditional name="adv_options">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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21 <param name="adv_options_selector" type="boolean" truevalue="use_adv_controls" label="Advanced controls" help="Allows you to specify options that are not listed above"/>
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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22 <when value="use_adv_controls">
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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23 <param name="scale_by" type="text" value="AF" label="scale sampling likelihood by this INFO field" help="-s, --scale-by; this only works for Float info fields such as AF" />
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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24 </when>
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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25 </conditional>
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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26 </inputs>
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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27 <outputs>
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28 <data format="vcf" name="out_file1" />
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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29 </outputs>
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30 <tests>
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31 <test>
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32 <param name="vcf_input" value="vcflib.vcf"/>
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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33 <param name="rate" value="0.2" />
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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34 <param name="random_seed" value="1" />
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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35 <param name="adv_options_selector" value="False" />
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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36 <output name="out_file1" file="vcfrandomsample-test1.vcf" lines_diff="2" />
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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37 </test>
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38 </tests>
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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39 <help>
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40
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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41 Randomly sample sites from an input VCF dataset. Scale the sampling probability by the field specified by --scale-by (see advanced controls). This may be
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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42 used to provide uniform sampling across allele frequencies, for instance (AF field in this case).
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43
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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44 Options::
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45
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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46 -r, --rate RATE base sampling probability per locus
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47 -s, --scale-by KEY scale sampling likelihood by this Float info field
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48 -p, --random-seed N use this random seed
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49
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50 ----
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51
ad12ba1db0e4 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 5a4e0ca9992af3a6e5ed2b533f04bb82ce761e0b
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52 Vcfrandomsample @IS_PART_OF_VCFLIB@
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53 </help>
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54 <expand macro="citations" />
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55 </tool>