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1
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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12
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4 <requirement type="package" version="2.0.10.3">macs2</requirement>
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1
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5 <requirement type="package" version="1.7.1">numpy</requirement>
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6 <yield />
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7 </requirements>
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8 </xml>
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9
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10 <xml name="conditional_effective_genome_size">
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11 <conditional name="effective_genome_size_options">
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12 <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="--gsize">
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13 <option value="3300000000">Human (3.300.000.000)</option>
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14 <option value="3000000000">Mouse (3.000.000.000)</option>
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15 <option value="190000000">Fly (190.000.000)</option>
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16 <option value="130000000">Worm (130.000.000)</option>
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17 <option value="user_defined">User defined</option>
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18 </param>
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19 <when value="user_defined">
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20 <param name="gsize" type="integer" size="12" label="Effective genome size" value=""/>
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21 </when>
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22 </conditional>
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23 </xml>
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24
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25 <token name="@effective_genome_size@">
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26 #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined':
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27 --gsize $effective_genome_size_options.gsize
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28 #else:
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29 --gsize $effective_genome_size_options.effective_genome_size_options_selector
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30 #end if
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31 </token>
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32
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33 <xml name="version_command">
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34 <version_command>macs2 --version</version_command>
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35 </xml>
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36
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37 <xml name="tag_size">
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38 <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will overide the auto detected tag size. DEFAULT: Not set (-1.0) (--tsize)" />
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39 </xml>
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40
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41 <xml name="stdio">
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42 <stdio>
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10
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43 <exit_code range="1:" />
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44 <exit_code range=":-1" />
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1
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45 <regex match="Error:" />
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10
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46 <regex match="Exception:" />
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1
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47 </stdio>
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48 </xml>
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9
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49
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50 <token name="@citation@">
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51 ------
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52
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53 **Citation**
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54
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55 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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56
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57 Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening.
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58 </token>
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1
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59 </macros>
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