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author iuc
date Mon, 26 Mar 2018 12:28:36 -0400
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iuc
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1 <tool id="vcfrandomsample" name="VCFrandomSample:" version="@WRAPPER_VERSION@+galaxy0">
1
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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>
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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 vcfrandomsample
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10 #if $adv_options.adv_options_selector == "use_adv_controls":
c035d96c5cbe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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11 -s "${adv_options.scale_by}"
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12 #end if
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13 -p ${random_seed}
c035d96c5cbe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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14 -r ${rate}
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15 "${vcf_input}" > "${out_file1}"
c035d96c5cbe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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16 </command>
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17 <inputs>
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18 <param format="vcf" name="vcf_input" type="data" label="Select random sites from"/>
c035d96c5cbe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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19 <param name="rate" type="float" value="0.1" label="base sampling probability per locus" help="-r, --rate"/>
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20 <param name="random_seed" type="integer" value="17823618326" label="use this random seed"
c035d96c5cbe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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21 help="-p, --random-seed; use this to make results reproducible" />
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22 <conditional name="adv_options">
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23 <param name="adv_options_selector" type="select" label="Advanced controls" help="Allows you to specify options that are not listed above">
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24 <option value="no">Don't use advanced options</option>
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25 <option value="use_adv_controls">Use advanced options</option>
c035d96c5cbe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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26 </param>
2
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27 <when value="no" />
1
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28 <when value="use_adv_controls">
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29 <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" />
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30 </when>
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31 </conditional>
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32 </inputs>
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33 <outputs>
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34 <data format="vcf" name="out_file1" />
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35 </outputs>
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36 <tests>
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37 <test>
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38 <param name="vcf_input" value="vcflib.vcf"/>
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39 <param name="rate" value="0.2" />
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40 <param name="random_seed" value="1" />
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41 <param name="adv_options_selector" value="no" />
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42 <output name="out_file1" file="vcfrandomsample-test1.vcf" lines_diff="2" />
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43 </test>
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44 </tests>
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45 <help>
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46 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
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47 used to provide uniform sampling across allele frequencies, for instance (AF field in this case).
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48
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49 ----
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50
c035d96c5cbe planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfrandomsample commit 0b9b6512272b82637c2f1e831367e89aed77ae79
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51 Vcfrandomsample @IS_PART_OF_VCFLIB@
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52 </help>
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53 <expand macro="citations" />
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54 </tool>