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1 <tool id="macs2_randsamoke" name="Randomly sample number or percentage" version="2.0.10.0">
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2 <description>of total reads</description>
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1
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3 <expand macro="requirements" />
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4 <expand macro="version_command" />
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5 <macros>
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6 <import>macs2_macros.xml</import>
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7 </macros>
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0
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8 <command>
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9 macs2 randsample
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10 -t $infile
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11 -o $outfile
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12
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13 --format '$ifile.extension.upper()'
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14
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15 --tsize $tsize
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16 #if str($method_options.method_options_selector ) == 'percentage':
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17 $method_options.percentage
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18 #else:
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19 $method_options.number
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20 #end if
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21
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22 </command>
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23 <inputs>
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24
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25 <!--may need to add a few more formats at later time-->
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26 <param name="infile" type="data" format="sam,bam,bed" label="Sequencing alignment file" />
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1
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27 <expand macro="tag_size" />
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0
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28
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29 <conditional name="method_options">
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30 <param name="method_options_selector" type="select" label="Select action to be performed">
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31 <option value="percentage">Percentage</option>
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32 <option value="number">Number</option>
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33 </param>
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34 <when value="percentage">
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35 <param name="percentage" type="float" value="80.0" label="Pvalue cutoff for binomial distribution test" help="(--percentage)" />
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36 </when>
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37 <when value="number">
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38 <param name="number" type="integer" value="800000" label="Number of tags you want to keep" help="Note that the number of tags in output is approximate as the number specified here (--number)" />
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39 </when>
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40 </conditional>
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41
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42 </inputs>
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43 <outputs>
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44 <data name="outfile" format="bed" label="${tool.name} on ${on_string}" />
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45 </outputs>
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46 <tests>
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47 <!--none yet for macs2-->
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48 </tests>
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49 <help>
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50 **What it does**
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51
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52 randsample tool from macs2
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53 ------
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54
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55 **Citation**
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56
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57 For the underlying tool, please cite Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9(9):R137.
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58
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59 Integration of MACS2 with Galaxy performed by Ziru Zhou ( ziruzhou@gmail.com ). Please send your comments/questions to modENCODE DCC at help@modencode.org.
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60 </help>
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61 </tool>
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