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1 <macros>
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3 <macro name="requirements">
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4 <requirements>
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5 <requirement type="package" version="1.7.1">numpy</requirement>
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6 <requirement type="package" version="2014-09-29">cistrome</requirement>
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7 </requirements>
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8 </macro>
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9 <macro name="requirements_seqpos">
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10 <requirements>
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11 <requirement type="package" version="1.7.1">numpy</requirement>
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12 <requirement type="package" version="2014-09-29">cistrome</requirement>
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13 <requirement type="package" version="2.7.3">jinja2</requirement>
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14 <requirement type="package" version="2.15.0">R</requirement>
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15 <requirement type="package" version="1.24.0">bioc_seqlogo</requirement>
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16 </requirements>
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17 </macro>
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18 <macro name="stdio">
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19 <stdio>
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20 <exit_code range=":-1" level="fatal" description="Error: Cannot open file" />
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21 <exit_code range="1:" level="fatal" description="Error" />
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22 </stdio>
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23 </macro>
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24 <macro name="refGenomeSourceConditional">
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25 <conditional name="refGenomeSource">
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26 <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Genome Reference Fasta sequence">
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27 <option value="cached" selected="True">Use a built-in genome</option>
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28 <option value="history">Use a genome from history</option>
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29 <option value="installed">cistrome installation</option>
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30 </param>
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31 <when value="cached">
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32 <param name="cistrome_assembly" type="select" label="Cistrome Genome Assembly">
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33 <options from_data_table="cistrome_assembly"/>
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34 </param>
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35 </when>
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36 <when value="history">
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37 <param name="ownFile" type="data" format="cistrome_assembly" metadata_name="dbkey" label="Select the reference genome" />
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38 </when> <!-- history -->
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39 <when value="installed">
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40 <param name="cistrome_static_assembly" type="select" label="Cistrome Genome Assembly">
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41 <option value="humanhg18">humanhg18</option>
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42 <option value="humanhg19">humanhg19</option>
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43 <option value="UCSC_MM7">UCSC_MM7</option>
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44 <option value="mousemm8_Mar2006">mousemm8_Mar2006</option>
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45 <option value="UCSC_MM9">UCSC_MM9</option>
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46 <option value="UCSC_CE4">UCSC_CE4</option>
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47 <option value="UCSC_CE6">UCSC_CE6</option>
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48 <option value="UCSC_DM3">UCSC_DM3</option>
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49 </param>
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50 </when> <!-- history -->
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51 </conditional> <!-- refGenomeSource -->
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52 </macro>
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53
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54 <template name="ref_genome_seq_opts">
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55 #if $refGenomeSource.genomeSource == 'cached':
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56 -g $refGenomeSource.cistrome_assembly.fields.path
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57 #elif $refGenomeSource.genomeSource == 'history':
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58 -g $refGenomeSource.ownFile.extra_files_path
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59 #else
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60 #if hasattr($__app__.config,'cistrome_static_library_path'):
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61 -g ${$__app__.config.cistrome_static_library_path}/assembly/$refGenomeSource.cistrome_static_assembly
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62 #elif $os.path.exists($os.path.join($__tool_data_path__,'assembly'))
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63 -g $__tool_data_path__/assembly/$refGenomeSource.cistrome_static_assembly
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64 #end if
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65 #end if
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66 </template>
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67
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68 <template name="script_chars">
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69 #set global $dollar = chr(36)
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70 #set global $gt = chr(62)
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71 #set global $lt = chr(60)
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72 #set global $ad = chr(38)
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73 </template>
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74
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75 <token name="@EXTERNAL_DOCUMENTATION@">
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76
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77 For details about this application, please go to:
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78 https://bitbucket.org/cistrome/cistrome-harvard/wiki/Home
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79
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80 </token>
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81 <token name="@CITATION_SECTION@">------
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82
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83 **Citation**
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84
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85 For the underlying tool, please cite the following publication:
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86 "Cistrome: an integrative platform for transcriptional regulation studies," Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y, Shin H, Wong SS, Ma J, Lei Y, Pape UJ, Poidinger M, Chen Y, Yeung K, Brown M, Turpaz Y, Liu XS. Genome Biol. 2011 Aug 22;12(8):R83.
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87
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88 </token>
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89 </macros>
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