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annotate create_reference_dataset.xml @ 13:3a4876d01c7e draft

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author jjohnson
date Tue, 12 Dec 2017 10:01:42 -0500
parents b22f8634ff84
children b67c24d902aa
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11
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1 <tool id="create_defuse_reference" name="Create DeFuse Reference" version="@DEFUSE_VERSION@.1">
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2 <description>create a defuse reference from Ensembl and UCSC sources</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 <requirements>
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7 <expand macro="defuse_requirement" />
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8 <expand macro="mapping_requirements" />
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9 </requirements>
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10 <command interpreter="command"> /bin/bash $defuse_script </command>
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11 <inputs>
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12 <conditional name="genome">
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13 <param name="choice" type="select" label="Select a Genome Build">
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14 <option value="GRCh38">Homo_sapiens GRCh38 hg38</option>
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15 <option value="GRCh37">Homo_sapiens GRCh37 hg19</option>
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16 <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
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17 <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
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18 <option value="NCBIM37">Mus_musculus NCBIM37 mm9</option>
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19 <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
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20 <option value="user_specified">User specified</option>
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21 </param>
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22 <when value="GRCh38">
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23 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
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24 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
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25 <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
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26 <param name="ensembl_version" type="hidden" value="80"/>
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27 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
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28 <param name="ncbi_prefix" type="hidden" value="Hs"/>
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29 <param name="ucsc_genome_version" type="hidden" value="hg38"/>
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30 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
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31 <param name="mt_chromosome" type="hidden" value="MT"/>
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32 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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33 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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34 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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35 </when>
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36 <when value="GRCh37">
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37 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
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38 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
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39 <param name="ensembl_genome_version" type="hidden" value="GRCh37"/>
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40 <param name="ensembl_version" type="hidden" value="71"/>
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41 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
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42 <param name="ncbi_prefix" type="hidden" value="Hs"/>
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43 <param name="ucsc_genome_version" type="hidden" value="hg19"/>
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44 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
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45 <param name="mt_chromosome" type="hidden" value="MT"/>
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46 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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47 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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48 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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49 </when>
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50 <when value="NCBI36">
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51 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
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52 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
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53 <param name="ensembl_genome_version" type="hidden" value="NCBI36"/>
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54 <param name="ensembl_version" type="hidden" value="54"/>
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55 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
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56 <param name="ncbi_prefix" type="hidden" value="Hs"/>
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57 <param name="ucsc_genome_version" type="hidden" value="hg18"/>
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58 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
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59 <param name="mt_chromosome" type="hidden" value="MT"/>
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60 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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61 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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62 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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63 </when>
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64 <when value="GRCm38">
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65 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
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66 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
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67 <param name="ensembl_genome_version" type="hidden" value="GRCm38"/>
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68 <param name="ensembl_version" type="hidden" value="71"/>
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69 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
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70 <param name="ncbi_prefix" type="hidden" value="Mm"/>
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71 <param name="ucsc_genome_version" type="hidden" value="mm10"/>
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72 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT"/>
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73 <param name="mt_chromosome" type="hidden" value="MT"/>
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74 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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75 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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76 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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77 </when>
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78 <when value="NCBIM37">
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79 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
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80 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
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81 <param name="ensembl_genome_version" type="hidden" value="NCBIM37"/>
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82 <param name="ensembl_version" type="hidden" value="67"/>
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83 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
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84 <param name="ncbi_prefix" type="hidden" value="Mm"/>
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85 <param name="ucsc_genome_version" type="hidden" value="mm9"/>
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86 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT"/>
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87 <param name="mt_chromosome" type="hidden" value="MT"/>
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88 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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89 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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90 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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91 </when>
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92 <when value="Rnor_5.0">
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93 <param name="ensembl_organism" type="hidden" value="rattus_norvegicus"/>
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94 <param name="ensembl_prefix" type="hidden" value="Rattus_norvegicus"/>
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95 <param name="ensembl_genome_version" type="hidden" value="Rnor_5.0"/>
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96 <param name="ensembl_version" type="hidden" value="71"/>
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97 <param name="ncbi_organism" type="hidden" value="Rattus_norvegicus"/>
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98 <param name="ncbi_prefix" type="hidden" value="Rn"/>
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99 <param name="ucsc_genome_version" type="hidden" value="rn5"/>
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100 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,MT"/>
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101 <param name="mt_chromosome" type="hidden" value="MT"/>
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102 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
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103 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
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104 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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105 </when>
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106 <when value="user_specified">
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107 <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name">
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108 <help>
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109 Examples: homo_sapiens, mus_musculus, rattus_norvegicus
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110 ftp://ftp.ensembl.org/pub/release-$ensembl_version/fasta/$ensembl_organism/dna/$ensembl_prefix.$ensembl_genome_version.$ensembl_version.dna.chromosome.$chromosome.fa.gz
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111 </help>
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112 </param>
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113 <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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114 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/>
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115 <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/>
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116 <param name="ncbi_organism" type="text" value="" label="NCBI Organism Name" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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117 <param name="ncbi_prefix" type="text" value="" label="NCBI Organism Unigene prefix" help="Examples: Hs, Mm, Rn"/>
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118 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg19, mm10, rn5"/>
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119 <param name="chromosomes" type="text" value="" label="Chromosomes for Ensembl genome build" >
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120 <help> Examples:
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121 Homo_sapiens: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT
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122 Mus_musculus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT
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123 Rattus_norvegicus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,MT
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124 ( ftp://ftp.ensembl.org/pub/release-71/fasta/homo_sapiens/dna/ )
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125 </help>
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126 </param>
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127 <param name="mt_chromosome" type="text" value="MT" label="Ensembl Mitochonrial Chromosome name" />
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128 <param name="gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding" label="Gene sources" />
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129 <param name="ig_gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene" label="IG Gene sources" />
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130 <param name="rrna_gene_sources" type="text" value="Mt_rRNA,rRNA,rRNA_pseudogene" label="Ribosomal Gene sources" />
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131 </when>
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132 </conditional>
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133 </inputs>
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134 <outputs>
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135 <data format="defuse.conf" name="config_txt" label="${tool.name} on ${genome.ensembl_genome_version} : config.txt"/>
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136 </outputs>
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137 <stdio>
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138 <exit_code range="1:" level="fatal" description="Error running Create DeFuse Reference" />
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139 <regex match="Error:"
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140 source="both"
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141 level="fatal"
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142 description="Error running Create DeFuse Reference" />
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143
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144 </stdio>
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145 <configfiles>
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146 <configfile name="defuse_config">
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147 #
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148 # Configuration file for defuse
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149 #
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150 # Variables that desiganate the PATH to an application, e.g. __SAMTOOLS_BIN__
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151 # will be set by the runtime script using the ENV PATH
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152 #
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153
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154 # Directory where the defuse code was unpacked
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155 source_directory = __DEFUSE_PATH__
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156
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157 # Organism IDs
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158 ensembl_organism = $genome.ensembl_organism
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159 ensembl_prefix = $genome.ensembl_prefix
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160 ensembl_version = $genome.ensembl_version
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161 ensembl_genome_version = $genome.ensembl_genome_version
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162 ucsc_genome_version = $genome.ucsc_genome_version
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163 ncbi_organism = $genome.ncbi_organism
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164 ncbi_prefix = $genome.ncbi_prefix
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165
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166 # Directory where you want your dataset
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167 dataset_directory = $config_txt.dataset.extra_files_path
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168
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169 #raw
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170 # Input genome and gene models
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171 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf
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172 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa
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173
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174 # Repeat table from ucsc genome browser
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175 repeats_filename = $(dataset_directory)/repeats.txt
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176
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177 # EST info downloaded from ucsc genome browser
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178 est_fasta = $(dataset_directory)/est.fa
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179 est_alignments = $(dataset_directory)/intronEst.txt
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180
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181 # Unigene clusters downloaded from ncbi
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182 unigene_fasta = $(dataset_directory)/$(ncbi_prefix).seq.uniq
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183 #end raw
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184
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185 # Paths to external tools
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186 samtools_bin = __SAMTOOLS_BIN__
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187 bowtie_bin = __BOWTIE_BIN__
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188 bowtie_build_bin = __BOWTIE_BUILD_BIN__
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189 blat_bin = __BLAT_BIN__
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190 fatotwobit_bin = __FATOTWOBIT_BIN__
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191 gmap_bin = __GMAP_BIN__
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192 gmap_setup_bin = __GMAP_SETUP_BIN__
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193 r_bin = __R_BIN__
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194 rscript_bin = __RSCRIPT_BIN__
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195
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196 #raw
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197 # Directory where you want your dataset
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198 gmap_index_directory = $(dataset_directory)/gmap
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199 #end raw
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200
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201 #raw
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202 # Dataset files
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203 dataset_prefix = $(dataset_directory)/defuse
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204 chromosome_prefix = $(dataset_prefix).dna.chromosomes
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205 exons_fasta = $(dataset_prefix).exons.fa
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206 cds_fasta = $(dataset_prefix).cds.fa
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207 cdna_regions = $(dataset_prefix).cdna.regions
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208 cdna_fasta = $(dataset_prefix).cdna.fa
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209 reference_fasta = $(dataset_prefix).reference.fa
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210 rrna_fasta = $(dataset_prefix).rrna.fa
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211 ig_gene_list = $(dataset_prefix).ig.gene.list
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212 repeats_regions = $(dataset_directory)/repeats.regions
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213 est_split_fasta1 = $(dataset_directory)/est.1.fa
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214 est_split_fasta2 = $(dataset_directory)/est.2.fa
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215 est_split_fasta3 = $(dataset_directory)/est.3.fa
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216 est_split_fasta4 = $(dataset_directory)/est.4.fa
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217 est_split_fasta5 = $(dataset_directory)/est.5.fa
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218 est_split_fasta6 = $(dataset_directory)/est.6.fa
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219 est_split_fasta7 = $(dataset_directory)/est.7.fa
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220 est_split_fasta8 = $(dataset_directory)/est.8.fa
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221 est_split_fasta9 = $(dataset_directory)/est.9.fa
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222
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223 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
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224 prefilter1 = $(unigene_fasta)
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225
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226 # deFuse scripts and tools
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227 scripts_directory = $(source_directory)/scripts
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228 tools_directory = $(source_directory)/tools
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229 data_directory = $(source_directory)/data
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230 #end raw
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231
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232 # Parameters for building the dataset
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233 chromosomes = $genome.chromosomes
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234 mt_chromosome = $genome.mt_chromosome
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235 gene_sources = $genome.gene_sources
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236 ig_gene_sources = $genome.ig_gene_sources
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237 rrna_gene_sources = $genome.rrna_gene_sources
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238 gene_biotypes = $genome.gene_sources
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239 ig_gene_biotypes = $genome.ig_gene_sources
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240 rrna_gene_biotypes = $genome.rrna_gene_sources
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241
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242 #raw
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243 # Remove temp files
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244 remove_job_files = yes
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245 remove_job_temp_files = yes
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246 #end raw
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247 </configfile>
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248 <configfile name="defuse_script">
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249 #!/bin/bash
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250 ## define some things for cheetah proccessing
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251 #set $amp = chr(38)
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252 #set $gt = chr(62)
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253 ## substitute pathnames into config file
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254 if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
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255 if `grep __SAMTOOLS_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi
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256 if `grep __BOWTIE_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
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257 if `grep __BOWTIE_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
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258 if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
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259 if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
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260 if `grep __GMAP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi
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261 if `grep __GMAP_SETUP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_SETUP_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_SETUP_BIN__#\${GMAP_SETUP_BIN}#" $defuse_config; fi
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262 if `grep __GMAP_INDEX_DIR__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $defuse_config; fi
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263 if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
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264 if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi
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265 ## copy config to output
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266 cp $defuse_config $config_txt
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267 ## make a data_dir and ln -s the input fastq
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268 mkdir -p $config_txt.dataset.extra_files_path
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269 ## create_reference_dataset.pl
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270 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config
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271 </configfile>
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272 </configfiles>
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273
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274 <tests>
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275 </tests>
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276 <help>
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277 **DeFuse**
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278
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279 DeFuse_ is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion. See the DeFuse_Version_0.6_ manual for details.
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280
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281 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.6_:
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282 - genome_fasta from Ensembl
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283 - gene_models from Ensembl
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284 - repeats_filename from UCSC RepeatMasker rmsk.txt
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285 - est_fasta from UCSC
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286 - est_alignments from UCSC intronEst.txt
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287 - unigene_fasta from NCBI
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288
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289 The create_defuse_reference Galaxy tool downloads the reference genome and other source files, and builds any derivative files including bowtie indices, gmap indices, and 2bit files. Expect this step to take at least 12 hours.
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290
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291
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292 It will generate a config.txt file that can be input into the deFuse Galaxy tool.
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293
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294 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
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295
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296 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
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297
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298 .. _DeFuse_Version_0.6: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1
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299
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300 ------
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301
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302 **Outputs**
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303
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304 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths.
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305
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306 </help>
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307 <expand macro="citations"/>
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308 </tool>