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17
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1 <macros>
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2 <xml name="requirements">
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3 <requirements>
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4 <requirement type="package" version="2.0.10.3">macs2</requirement>
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5 <requirement type="package" version="1.7.1">numpy</requirement>
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18
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6 <requirement type="package" version="0.12.0">scipy</requirement>
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17
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7 <yield />
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8 </requirements>
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9 </xml>
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10
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11 <xml name="conditional_effective_genome_size">
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12 <conditional name="effective_genome_size_options">
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13 <param name="effective_genome_size_options_selector" type="select" label="Effective genome size" help="--gsize">
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19
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14 <option value="2451960000">Human (2.451.960.000)</option>
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15 <option value="2150570000">Mouse (2.150.570.000)</option>
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16 <option value="121400000">Fly (121.400.000)</option>
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17 <option value="93260000">Worm (93.260.000)</option>
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17
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18 <option value="user_defined">User defined</option>
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19 </param>
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20 <when value="user_defined">
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21 <param name="gsize" type="integer" size="12" label="Effective genome size" value=""/>
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22 </when>
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23 </conditional>
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24 </xml>
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25
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26 <token name="@effective_genome_size@">
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27 #if $effective_genome_size_options.effective_genome_size_options_selector == 'user_defined':
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19
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28 --gsize "${ effective_genome_size_options.gsize }"
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17
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29 #else:
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19
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30 --gsize "${ effective_genome_size_options.effective_genome_size_options_selector }"
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17
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31 #end if
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32 </token>
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33
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34 <xml name="version_command">
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35 <version_command>macs2 --version</version_command>
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36 </xml>
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37
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38 <xml name="tag_size">
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39 <param name="tsize" type="float" label="Tag size" value="-1.0" help="This will overide the auto detected tag size. Per default that option is deactivated: -1.0 (--tsize)" />
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40 </xml>
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41 <xml name="band_width">
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42 <param name="band_width" type="integer" value="300" label="Band width for picking regions to compute fragment size"
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43 help="This value is only used while building the shifting model. (--bw)" />
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44 </xml>
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45
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46 <token name="@tag_size@">
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47 #if $tsize == -1.0:
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19
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48 --tsize "${ tsize }"
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17
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49 #end if
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50 </token>
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51
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52 <xml name="stdio">
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53 <stdio>
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54 <exit_code range="1:" />
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55 <exit_code range=":-1" />
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56 <regex match="Error:" />
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57 <regex match="Exception:" />
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58 </stdio>
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59 </xml>
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60
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61 <token name="@citation@">
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62 ------
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63
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64 **Citation**
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65
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66 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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67
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68 Integration of MACS2 with Galaxy performed by Ziru Zhou and Bjoern Gruening.
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69 </token>
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70 </macros>
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