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author jjohnson
date Thu, 19 Oct 2017 10:05:54 -0400
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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 </requirements>
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9 <command interpreter="command"> /bin/bash $defuse_script </command>
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10 <inputs>
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11 <conditional name="genome">
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12 <param name="choice" type="select" label="Select a Genome Build">
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13 <option value="GRCh38">Homo_sapiens GRCh38 hg38</option>
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14 <option value="GRCh37">Homo_sapiens GRCh37 hg19</option>
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15 <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
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16 <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
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17 <option value="NCBIM37">Mus_musculus NCBIM37 mm9</option>
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18 <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
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19 <option value="user_specified">User specified</option>
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20 </param>
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21 <when value="GRCh38">
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22 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
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23 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
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24 <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
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25 <param name="ensembl_version" type="hidden" value="80"/>
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26 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
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27 <param name="ncbi_prefix" type="hidden" value="Hs"/>
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28 <param name="ucsc_genome_version" type="hidden" value="hg38"/>
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29 <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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30 <param name="mt_chromosome" type="hidden" value="MT"/>
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31 <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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32 <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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33 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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34 </when>
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35 <when value="GRCh37">
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36 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
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37 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
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38 <param name="ensembl_genome_version" type="hidden" value="GRCh37"/>
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39 <param name="ensembl_version" type="hidden" value="71"/>
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40 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
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41 <param name="ncbi_prefix" type="hidden" value="Hs"/>
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42 <param name="ucsc_genome_version" type="hidden" value="hg19"/>
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43 <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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44 <param name="mt_chromosome" type="hidden" value="MT"/>
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45 <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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46 <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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47 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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48 </when>
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49 <when value="NCBI36">
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50 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
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51 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
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52 <param name="ensembl_genome_version" type="hidden" value="NCBI36"/>
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53 <param name="ensembl_version" type="hidden" value="54"/>
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54 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
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55 <param name="ncbi_prefix" type="hidden" value="Hs"/>
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56 <param name="ucsc_genome_version" type="hidden" value="hg18"/>
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57 <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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58 <param name="mt_chromosome" type="hidden" value="MT"/>
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59 <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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60 <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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61 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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62 </when>
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63 <when value="GRCm38">
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64 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
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65 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
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66 <param name="ensembl_genome_version" type="hidden" value="GRCm38"/>
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67 <param name="ensembl_version" type="hidden" value="71"/>
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68 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
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69 <param name="ncbi_prefix" type="hidden" value="Mm"/>
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70 <param name="ucsc_genome_version" type="hidden" value="mm10"/>
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71 <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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72 <param name="mt_chromosome" type="hidden" value="MT"/>
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73 <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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74 <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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75 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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76 </when>
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77 <when value="NCBIM37">
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78 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
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79 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
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80 <param name="ensembl_genome_version" type="hidden" value="NCBIM37"/>
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81 <param name="ensembl_version" type="hidden" value="67"/>
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82 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
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83 <param name="ncbi_prefix" type="hidden" value="Mm"/>
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84 <param name="ucsc_genome_version" type="hidden" value="mm9"/>
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85 <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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86 <param name="mt_chromosome" type="hidden" value="MT"/>
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87 <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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88 <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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89 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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90 </when>
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91 <when value="Rnor_5.0">
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92 <param name="ensembl_organism" type="hidden" value="rattus_norvegicus"/>
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93 <param name="ensembl_prefix" type="hidden" value="Rattus_norvegicus"/>
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94 <param name="ensembl_genome_version" type="hidden" value="Rnor_5.0"/>
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95 <param name="ensembl_version" type="hidden" value="71"/>
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96 <param name="ncbi_organism" type="hidden" value="Rattus_norvegicus"/>
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97 <param name="ncbi_prefix" type="hidden" value="Rn"/>
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98 <param name="ucsc_genome_version" type="hidden" value="rn5"/>
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99 <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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100 <param name="mt_chromosome" type="hidden" value="MT"/>
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101 <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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102 <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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103 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
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104 </when>
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105 <when value="user_specified">
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106 <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name">
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107 <help>
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108 Examples: homo_sapiens, mus_musculus, rattus_norvegicus
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109 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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110 </help>
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111 </param>
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112 <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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113 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/>
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114 <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/>
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115 <param name="ncbi_organism" type="text" value="" label="NCBI Organism Name" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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116 <param name="ncbi_prefix" type="text" value="" label="NCBI Organism Unigene prefix" help="Examples: Hs, Mm, Rn"/>
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117 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg19, mm10, rn5"/>
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118 <param name="chromosomes" type="text" value="" label="Chromosomes for Ensembl genome build" >
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119 <help> Examples:
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120 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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121 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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122 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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123 ( ftp://ftp.ensembl.org/pub/release-71/fasta/homo_sapiens/dna/ )
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124 </help>
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125 </param>
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126 <param name="mt_chromosome" type="text" value="MT" label="Ensembl Mitochonrial Chromosome name" />
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127 <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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128 <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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129 <param name="rrna_gene_sources" type="text" value="Mt_rRNA,rRNA,rRNA_pseudogene" label="Ribosomal Gene sources" />
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130 </when>
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131 </conditional>
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132 </inputs>
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133 <outputs>
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134 <data format="defuse.conf" name="config_txt" label="${tool.name} on ${genome.ensembl_genome_version} : config.txt"/>
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135 </outputs>
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136 <stdio>
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137 <exit_code range="1:" level="fatal" description="Error running Create DeFuse Reference" />
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138 <regex match="Error:"
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139 source="both"
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140 level="fatal"
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141 description="Error running Create DeFuse Reference" />
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142
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143 </stdio>
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144 <configfiles>
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145 <configfile name="defuse_config">
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146 #
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147 # Configuration file for defuse
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148 #
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149 # Variables that desiganate the PATH to an application, e.g. __SAMTOOLS_BIN__
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150 # will be set by the runtime script using the ENV PATH
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151 #
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152
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153 # Directory where the defuse code was unpacked
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154 source_directory = __DEFUSE_PATH__
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155
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156 # Organism IDs
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157 ensembl_organism = $genome.ensembl_organism
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158 ensembl_prefix = $genome.ensembl_prefix
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159 ensembl_version = $genome.ensembl_version
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160 ensembl_genome_version = $genome.ensembl_genome_version
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161 ucsc_genome_version = $genome.ucsc_genome_version
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162 ncbi_organism = $genome.ncbi_organism
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163 ncbi_prefix = $genome.ncbi_prefix
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164
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165 # Directory where you want your dataset
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166 dataset_directory = $config_txt.dataset.extra_files_path
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167
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168 #raw
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169 # Input genome and gene models
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170 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf
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171 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa
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172
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173 # Repeat table from ucsc genome browser
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174 repeats_filename = $(dataset_directory)/repeats.txt
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175
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176 # EST info downloaded from ucsc genome browser
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177 est_fasta = $(dataset_directory)/est.fa
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178 est_alignments = $(dataset_directory)/intronEst.txt
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179
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180 # Unigene clusters downloaded from ncbi
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181 unigene_fasta = $(dataset_directory)/$(ncbi_prefix).seq.uniq
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182 #end raw
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183
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184 # Paths to external tools
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185 samtools_bin = __SAMTOOLS_BIN__
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186 bowtie_bin = __BOWTIE_BIN__
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187 bowtie_build_bin = __BOWTIE_BUILD_BIN__
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188 blat_bin = __BLAT_BIN__
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189 fatotwobit_bin = __FATOTWOBIT_BIN__
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190 gmap_bin = __GMAP_BIN__
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191 gmap_setup_bin = __GMAP_SETUP_BIN__
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192 r_bin = __R_BIN__
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193 rscript_bin = __RSCRIPT_BIN__
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194
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195 #raw
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196 # Directory where you want your dataset
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197 gmap_index_directory = $(dataset_directory)/gmap
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198 #end raw
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199
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200 #raw
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201 # Dataset files
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202 dataset_prefix = $(dataset_directory)/defuse
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203 chromosome_prefix = $(dataset_prefix).dna.chromosomes
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204 exons_fasta = $(dataset_prefix).exons.fa
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205 cds_fasta = $(dataset_prefix).cds.fa
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206 cdna_regions = $(dataset_prefix).cdna.regions
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207 cdna_fasta = $(dataset_prefix).cdna.fa
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208 reference_fasta = $(dataset_prefix).reference.fa
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209 rrna_fasta = $(dataset_prefix).rrna.fa
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210 ig_gene_list = $(dataset_prefix).ig.gene.list
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211 repeats_regions = $(dataset_directory)/repeats.regions
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212 est_split_fasta1 = $(dataset_directory)/est.1.fa
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213 est_split_fasta2 = $(dataset_directory)/est.2.fa
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214 est_split_fasta3 = $(dataset_directory)/est.3.fa
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215 est_split_fasta4 = $(dataset_directory)/est.4.fa
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216 est_split_fasta5 = $(dataset_directory)/est.5.fa
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217 est_split_fasta6 = $(dataset_directory)/est.6.fa
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218 est_split_fasta7 = $(dataset_directory)/est.7.fa
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219 est_split_fasta8 = $(dataset_directory)/est.8.fa
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220 est_split_fasta9 = $(dataset_directory)/est.9.fa
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221
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222 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
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223 prefilter1 = $(unigene_fasta)
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224
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225 # deFuse scripts and tools
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226 scripts_directory = $(source_directory)/scripts
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227 tools_directory = $(source_directory)/tools
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228 data_directory = $(source_directory)/data
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229 #end raw
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230
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231 # Parameters for building the dataset
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232 chromosomes = $genome.chromosomes
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233 mt_chromosome = $genome.mt_chromosome
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234 gene_sources = $genome.gene_sources
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235 ig_gene_sources = $genome.ig_gene_sources
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236 rrna_gene_sources = $genome.rrna_gene_sources
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237 gene_biotypes = $genome.gene_sources
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238 ig_gene_biotypes = $genome.ig_gene_sources
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239 rrna_gene_biotypes = $genome.rrna_gene_sources
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240
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241 #raw
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242 # Remove temp files
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243 remove_job_files = yes
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244 remove_job_temp_files = yes
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245 #end raw
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246 </configfile>
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247 <configfile name="defuse_script">
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248 #!/bin/bash
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249 ## define some things for cheetah proccessing
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250 #set $amp = chr(38)
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251 #set $gt = chr(62)
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252 ## substitute pathnames into config file
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253 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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254 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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255 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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256 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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257 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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258 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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259 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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260 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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261 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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262 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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263 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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264 ## copy config to output
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265 cp $defuse_config $config_txt
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266 ## make a data_dir and ln -s the input fastq
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267 mkdir -p $config_txt.dataset.extra_files_path
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268 ## create_reference_dataset.pl
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269 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config
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270 </configfile>
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271 </configfiles>
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272
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273 <tests>
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274 </tests>
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275 <help>
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276 **DeFuse**
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277
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278 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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279
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280 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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281 - genome_fasta from Ensembl
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282 - gene_models from Ensembl
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283 - repeats_filename from UCSC RepeatMasker rmsk.txt
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284 - est_fasta from UCSC
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285 - est_alignments from UCSC intronEst.txt
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286 - unigene_fasta from NCBI
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287
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288 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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289
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290
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291 It will generate a config.txt file that can be input into the deFuse Galaxy tool.
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292
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293 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
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294
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295 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
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296
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297 .. _DeFuse_Version_0.6: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1
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298
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299 ------
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300
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301 **Outputs**
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302
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303 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths.
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304
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305 </help>
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306 <expand macro="citations"/>
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307 </tool>