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annotate create_reference_dataset.xml @ 34:3099cec648e7

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Update tool_dependencies, add help
author Jim Johnson <jj@umn.edu>
date Tue, 15 Oct 2013 17:02:23 -0500
parents 1af6f32ff592
children a004033614d4
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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 $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="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">
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93 <help>
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94 Examples: homo_sapiens, mus_musculus, rattus_norvegicus
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95 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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96 </help>
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97 </param>
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98 <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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99 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/>
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100 <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/>
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101 <param name="ncbi_organism" type="text" value="" label="NCBI Organism Name" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
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102 <param name="ncbi_prefix" type="text" value="" label="NCBI Organism Unigene prefix" help="Examples: Hs, Mm, Rn"/>
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103 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg19, mm10, rn5"/>
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104 <param name="chromosomes" type="text" value="" label="Chromosomes for Ensembl genome build" >
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105 <help> Examples:
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106 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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107 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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108 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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109 ( ftp://ftp.ensembl.org/pub/release-71/fasta/homo_sapiens/dna/ )
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110 </help>
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111 </param>
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112 <param name="mt_chromosome" type="text" value="MT" label="Ensembl Mitochonrial Chromosome name" />
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113 <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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114 <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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115 <param name="rrna_gene_sources" type="text" value="Mt_rRNA,rRNA,rRNA_pseudogene" label="Ribosomal Gene sources" />
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116 </when>
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117 </conditional>
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118 </inputs>
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119 <outputs>
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120 <data format="defuse.conf" name="config_txt" label="${tool.name} on ${genome.ensembl_genome_version} : config.txt"/>
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121 </outputs>
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122 <stdio>
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123 <exit_code range="1:" level="fatal" description="Error running Create DeFuse Reference" />
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124 <regex match="Error:"
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125 source="both"
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126 level="fatal"
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127 description="Error running Create DeFuse Reference" />
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128
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129 </stdio>
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130 <configfiles>
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131 <configfile name="defuse_config">
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132 #
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133 # Configuration file for defuse
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134 #
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135 # Variables that desiganate the PATH to an application, e.g. __SAMTOOLS_BIN__
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136 # will be set by the runtime script using the ENV PATH
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137 #
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138
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139 # Directory where the defuse code was unpacked
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140 source_directory = __DEFUSE_PATH__
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141
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142 # Organism IDs
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143 ensembl_organism = $genome.ensembl_organism
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144 ensembl_prefix = $genome.ensembl_prefix
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145 ensembl_version = $genome.ensembl_version
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146 ensembl_genome_version = $genome.ensembl_genome_version
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147 ucsc_genome_version = $genome.ucsc_genome_version
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148 ncbi_organism = $genome.ncbi_organism
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149 ncbi_prefix = $genome.ncbi_prefix
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150
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151 # Directory where you want your dataset
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152 dataset_directory = $config_txt.extra_files_path
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153
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154 #raw
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155 # Input genome and gene models
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156 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf
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157 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa
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158
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159 # Repeat table from ucsc genome browser
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160 repeats_filename = $(dataset_directory)/repeats.txt
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161
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162 # EST info downloaded from ucsc genome browser
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163 est_fasta = $(dataset_directory)/est.fa
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164 est_alignments = $(dataset_directory)/intronEst.txt
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165
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166 # Unigene clusters downloaded from ncbi
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167 unigene_fasta = $(dataset_directory)/$(ncbi_prefix).seq.uniq
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168 #end raw
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169
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170 # Paths to external tools
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171 samtools_bin = __SAMTOOLS_BIN__
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172 bowtie_bin = __BOWTIE_BIN__
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173 bowtie_build_bin = __BOWTIE_BUILD_BIN__
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174 blat_bin = __BLAT_BIN__
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175 fatotwobit_bin = __FATOTWOBIT_BIN__
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176 gmap_bin = __GMAP_BIN__
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177 gmap_setup_bin = __GMAP_SETUP_BIN__
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178 r_bin = __R_BIN__
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179 rscript_bin = __RSCRIPT_BIN__
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180
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181 #raw
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182 # Directory where you want your dataset
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183 gmap_index_directory = $(dataset_directory)/gmap
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184 #end raw
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185
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186 #raw
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187 # Dataset files
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188 dataset_prefix = $(dataset_directory)/defuse
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189 chromosome_prefix = $(dataset_prefix).dna.chromosomes
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190 exons_fasta = $(dataset_prefix).exons.fa
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191 cds_fasta = $(dataset_prefix).cds.fa
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192 cdna_regions = $(dataset_prefix).cdna.regions
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193 cdna_fasta = $(dataset_prefix).cdna.fa
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194 reference_fasta = $(dataset_prefix).reference.fa
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195 rrna_fasta = $(dataset_prefix).rrna.fa
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196 ig_gene_list = $(dataset_prefix).ig.gene.list
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197 repeats_regions = $(dataset_directory)/repeats.regions
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198 est_split_fasta1 = $(dataset_directory)/est.1.fa
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199 est_split_fasta2 = $(dataset_directory)/est.2.fa
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200 est_split_fasta3 = $(dataset_directory)/est.3.fa
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201 est_split_fasta4 = $(dataset_directory)/est.4.fa
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202 est_split_fasta5 = $(dataset_directory)/est.5.fa
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203 est_split_fasta6 = $(dataset_directory)/est.6.fa
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204 est_split_fasta7 = $(dataset_directory)/est.7.fa
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205 est_split_fasta8 = $(dataset_directory)/est.8.fa
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206 est_split_fasta9 = $(dataset_directory)/est.9.fa
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207
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208 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
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209 prefilter1 = $(unigene_fasta)
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210
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211 # deFuse scripts and tools
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212 scripts_directory = $(source_directory)/scripts
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213 tools_directory = $(source_directory)/tools
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214 data_directory = $(source_directory)/data
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215 #end raw
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216
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217 # Parameters for building the dataset
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218 chromosomes = $genome.chromosomes
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219 mt_chromosome = $genome.mt_chromosome
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220 gene_sources = $genome.gene_sources
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221 ig_gene_sources = $genome.ig_gene_sources
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222 rrna_gene_sources = $genome.rrna_gene_sources
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223
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224 #raw
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225 # Remove temp files
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226 remove_job_files = yes
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227 remove_job_temp_files = yes
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228 #end raw
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229 </configfile>
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230 <configfile name="defuse_script">
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231 #!/bin/bash
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232 ## define some things for cheetah proccessing
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233 #set $amp = chr(38)
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234 #set $gt = chr(62)
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235 ## substitute pathnames into config file
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236 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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237 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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238 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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239 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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240 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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241 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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242 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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243 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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244 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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245 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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246 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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247 ## copy config to output
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248 cp $defuse_config $config_txt
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249 ## make a data_dir and ln -s the input fastq
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250 mkdir -p $config_txt.extra_files_path
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251 ## create_reference_dataset.pl
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252 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config
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253 </configfile>
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254 </configfiles>
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255
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256 <tests>
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257 </tests>
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258 <help>
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259 **DeFuse**
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260
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261 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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262
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263 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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264 - genome_fasta from Ensembl
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265 - gene_models from Ensembl
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266 - repeats_filename from UCSC RepeatMasker rmsk.txt
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267 - est_fasta from UCSC
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268 - est_alignments from UCSC intronEst.txt
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269 - unigene_fasta from NCBI
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270
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271 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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272
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273
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274 It will generate a config.txt file that can be input into the deFuse Galaxy tool.
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275
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276 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
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277
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278 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
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279
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280 .. _DeFuse_Version_0.6: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1
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281
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282 ------
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283
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284 **Outputs**
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285
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286 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths.
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287
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288 </help>
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289 </tool>