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annotate create_reference_dataset.xml @ 18:547d8db4673e

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Update create_reference_dataset for non human genome builds
author Jim Johnson <jj@umn.edu>
date Sat, 15 Jun 2013 14:36:47 -0500
parents d975e466d443
children 1af6f32ff592
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85693cb5339f Correct tool_id create_reference_dataset.xml
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1 <tool id="create_defuse_reference" name="Create DeFuse Reference" version="1.6.1">
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2 <description>create a defuse reference from Ensembl and UCSC sources</description>
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3 <requirements>
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4 <requirement type="package" version="0.6.1">defuse</requirement>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 <requirement type="package" version="1.0.0">bowtie</requirement>
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7 <requirement type="package" version="2013-05-09">gmap</requirement>
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8 <requirement type="package" version="latest">kent</requirement>
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9 </requirements>
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10 <command interpreter="command"> /bin/bash $shscript </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="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="GRCh37">
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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="GRCh37"/>
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25 <param name="ensembl_version" type="hidden" value="71"/>
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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="hg19"/>
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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="NCBI36">
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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="NCBI36"/>
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39 <param name="ensembl_version" type="hidden" value="54"/>
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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="hg18"/>
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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="GRCm38">
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50 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
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51 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
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52 <param name="ensembl_genome_version" type="hidden" value="GRCm38"/>
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53 <param name="ensembl_version" type="hidden" value="71"/>
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54 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
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55 <param name="ncbi_prefix" type="hidden" value="Mm"/>
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56 <param name="ucsc_genome_version" type="hidden" value="mm10"/>
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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,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="NCBIM37">
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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="NCBIM37"/>
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67 <param name="ensembl_version" type="hidden" value="67"/>
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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="mm9"/>
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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="Rnor_5.0">
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78 <param name="ensembl_organism" type="hidden" value="rattus_norvegicus"/>
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79 <param name="ensembl_prefix" type="hidden" value="Rattus_norvegicus"/>
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80 <param name="ensembl_genome_version" type="hidden" value="Rnor_5.0"/>
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81 <param name="ensembl_version" type="hidden" value="71"/>
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82 <param name="ncbi_organism" type="hidden" value="Rattus_norvegicus"/>
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83 <param name="ncbi_prefix" type="hidden" value="Rn"/>
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84 <param name="ucsc_genome_version" type="hidden" value="rn5"/>
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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,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="user_specified">
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92 <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name" help="Examples: homo_sapiens, mus_musculus, rattus_norvegicus"/>
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93 <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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94 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/>
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95 <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/>
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96 <param name="ncbi_organism" type="text" value="" label="NCBI Organism Name" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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97 <param name="ncbi_prefix" type="text" value="" label="NCBI Organism Unigene prefix" help="Examples: Hs, Mm, Rn"/>
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98 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg19, mm10, rn5"/>
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99 <param name="chromosomes" type="text" value="" label="Chromosomes for Ensembl genome build" >
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100 <help> Examples:
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101 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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102 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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103 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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104 ( ftp://ftp.ensembl.org/pub/release-71/fasta/homo_sapiens/dna/ )
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105 </help>
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106 </param>
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107 <param name="mt_chromosome" type="text" value="MT" label="Ensembl Mitochonrial Chromosome name" />
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108 <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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109 <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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110 <param name="rrna_gene_sources" type="text" value="Mt_rRNA,rRNA,rRNA_pseudogene" label="Ribosomal Gene sources" />
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111 </when>
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112 </conditional>
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113 </inputs>
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114 <outputs>
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115 <data format="txt" name="config_txt" label="${tool.name} on ${on_string}: config.txt"/>
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116 </outputs>
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117 <stdio>
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118 <exit_code range="1:" level="fatal" description="Error running Create DeFuse Reference" />
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119 <regex match="Error:"
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120 source="both"
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121 level="fatal"
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122 description="Error running Create DeFuse Reference" />
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123
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124 </stdio>
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125 <configfiles>
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126 <configfile name="defuse_config">
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127 #import ast
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128 #
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129 # Configuration file for defuse
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130 #
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131 # At a minimum, change all values enclused by []
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132 #
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133
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134 # Directory where the defuse code was unpacked
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135 ## Default location in the tool/defuse directory
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136 # source_directory = ${__root_dir__}/tools/defuse
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137 source_directory = __DEFUSE_PATH__
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138
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139 ensembl_organism = $genome.ensembl_organism
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140 ensembl_prefix = $genome.ensembl_prefix
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141 ensembl_version = $genome.ensembl_version
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142 ensembl_genome_version = $genome.ensembl_genome_version
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143 ucsc_genome_version = $genome.ucsc_genome_version
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144 ncbi_organism = $genome.ncbi_organism
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145 ncbi_prefix = $genome.ncbi_prefix
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146
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147 # Directory where you want your dataset
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148 dataset_directory = $config_txt.extra_files_path
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149
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150 #raw
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151 # Input genome and gene models
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152 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf
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153 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa
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154
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155 # Repeat table from ucsc genome browser
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156 repeats_filename = $(dataset_directory)/repeats.txt
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157
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158 # EST info downloaded from ucsc genome browser
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159 est_fasta = $(dataset_directory)/est.fa
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160 est_alignments = $(dataset_directory)/intronEst.txt
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161
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162 # Unigene clusters downloaded from ncbi
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163 unigene_fasta = $(dataset_directory)/$(ncbi_prefix).seq.uniq
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164 #end raw
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165
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166 # Paths to external tools
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167 samtools_bin = __SAMTOOLS_BIN__
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168 bowtie_bin = __BOWTIE_BIN__
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169 bowtie_build_bin = __BOWTIE_BUILD_BIN__
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170 blat_bin = __BLAT_BIN__
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171 fatotwobit_bin = __FATOTWOBIT_BIN__
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172 gmap_bin = __GMAP_BIN__
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173 gmap_setup_bin = __GMAP_SETUP_BIN__
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174 r_bin = __R_BIN__
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175 rscript_bin = __RSCRIPT_BIN__
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176
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177 #raw
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178 # Directory where you want your dataset
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179 gmap_index_directory = $(dataset_directory)/gmap
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180 #end raw
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181
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182 #raw
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183 # Dataset files
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184 dataset_prefix = $(dataset_directory)/defuse
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185 chromosome_prefix = $(dataset_prefix).dna.chromosomes
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186 exons_fasta = $(dataset_prefix).exons.fa
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187 cds_fasta = $(dataset_prefix).cds.fa
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188 cdna_regions = $(dataset_prefix).cdna.regions
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189 cdna_fasta = $(dataset_prefix).cdna.fa
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190 reference_fasta = $(dataset_prefix).reference.fa
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191 rrna_fasta = $(dataset_prefix).rrna.fa
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192 ig_gene_list = $(dataset_prefix).ig.gene.list
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193 repeats_regions = $(dataset_directory)/repeats.regions
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194 est_split_fasta1 = $(dataset_directory)/est.1.fa
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195 est_split_fasta2 = $(dataset_directory)/est.2.fa
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196 est_split_fasta3 = $(dataset_directory)/est.3.fa
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197 est_split_fasta4 = $(dataset_directory)/est.4.fa
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198 est_split_fasta5 = $(dataset_directory)/est.5.fa
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199 est_split_fasta6 = $(dataset_directory)/est.6.fa
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200 est_split_fasta7 = $(dataset_directory)/est.7.fa
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201 est_split_fasta8 = $(dataset_directory)/est.8.fa
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202 est_split_fasta9 = $(dataset_directory)/est.9.fa
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203
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204 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
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205 prefilter1 = $(unigene_fasta)
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206
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207 # deFuse scripts and tools
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208 scripts_directory = $(source_directory)/scripts
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209 tools_directory = $(source_directory)/tools
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210 data_directory = $(source_directory)/data
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211 #end raw
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212
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213 #raw
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214 # Bowtie parameters
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215 bowtie_threads = 1
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216 bowtie_quals = --phred33-quals
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217 max_insert_size = 500
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218 #end raw
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219
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220 # Parameters for building the dataset
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221 chromosomes = $genome.chromosomes
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222 mt_chromosome = $genome.mt_chromosome
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223 gene_sources = $genome.gene_sources
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224 ig_gene_sources = $genome.ig_gene_sources
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225 rrna_gene_sources = $genome.rrna_gene_sources
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226
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227 #raw
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228 # Blat sequences per job
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229 num_blat_sequences = 10000
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230
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231 # Minimum gene fusion range
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232 dna_concordant_length = 2000
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233
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234 # Trim length for discordant reads (split reads are not trimmed)
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235 discord_read_trim = 50
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236
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237 # Calculate extra annotations, fusion splice index and interrupted index
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238 calculate_extra_annotations = no
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239
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240 # Filtering parameters
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241 clustering_precision = 0.95
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242 span_count_threshold = 5
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243 percent_identity_threshold = 0.90
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244 split_min_anchor = 4
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245 splice_bias = 10
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246 positive_controls = $(data_directory)/controls.txt
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247 probability_threshold = 0.50
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248
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249 # Position density when calculating covariance
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250 covariance_sampling_density = 0.01
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251
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252 # Number of reads for each job in split
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253 reads_per_job = 1000000
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254
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255 # If you have command line 'mail' and wish to be notified
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256 mailto = andrew.mcpherson@gmail.com
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257
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258 # Remove temp files
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259 remove_job_files = yes
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260 remove_job_temp_files = yes
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261 #end raw
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262 </configfile>
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263 <configfile name="shscript">
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264 #!/bin/bash
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265 ## define some things for cheetah proccessing
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266 #set $amp = chr(38)
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267 #set $gt = chr(62)
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268 ## substitute pathnames into config file
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269 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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270 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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271 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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272 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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273 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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274 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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275 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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276 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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277 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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278 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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279 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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280 ## copy config to output
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281 cp $defuse_config $config_txt
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282 ## make a data_dir and ln -s the input fastq
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283 mkdir -p $config_txt.extra_files_path
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284 ## create_reference_dataset.pl
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285 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config
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286 </configfile>
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287 </configfiles>
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288
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289 <tests>
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290 </tests>
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291 <help>
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292 **DeFuse**
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293
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294 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_0.6.1_ manual for details.
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295
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296 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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297 - genome_fasta from Ensembl
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298 - gene_models from Ensembl
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299 - repeats_filename from UCSC RepeatMasker rmsk.txt
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300 - est_fasta from UCSC
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301 - est_alignments from UCSC intronEst.txt
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302 - unigene_fasta from NCBI
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303
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304 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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305
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306
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307 It will generate a config.txt file that can be input into the deFuse Galaxy tool.
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308
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309 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
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310
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311 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
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312
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313 .. _DeFuse_Version_0.6: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1
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314
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315 ------
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316
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317 **Outputs**
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318
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319 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths.
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320
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321 </help>
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322 </tool>