defuse: datamanager_create_reference.xml annotate

annotate datamanager_create_reference.xml @ 41:74de1ccc51db

Add GRCh38 hg38, minor fixes.

author	Jim Johnson <jj@umn.edu>
date	Fri, 18 Dec 2015 14:37:33 -0600
parents	68494d6aabeb
children	aedaa66483f1

rev	line source
19 1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	1 <tool id="data_manager_defuse_reference" name="DeFuse Reference DataManager" version="1.6.1" tool_type="manage_data">
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	2 <description>create a defuse reference from Ensembl and UCSC sources</description>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	3 <requirements>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	4 <requirement type="package" version="0.6.1">defuse</requirement>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	5 <requirement type="package" version="0.1.18">samtools</requirement>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	6 <requirement type="package" version="1.0.0">bowtie</requirement>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	7 <requirement type="package" version="2013-05-09">gmap</requirement>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	8 <requirement type="package" version="latest">kent</requirement>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	9 </requirements>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	10 <command interpreter="python"> datamanager_create_reference.py
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	11 --dbkey $genome.ensembl_genome_version
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	12 --description "$genome.ensembl_prefix $genome.ensembl_genome_version ($genome.ucsc_genome_version)"
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	13 --defuse_config $defuse_config
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	14 --defuse_script $defuse_script
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	15 $out_file
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	16 </command>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	17 <inputs>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	18 <conditional name="genome">
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	19 <param name="choice" type="select" label="Select a Genome Build">
41 74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	20 <option value="GRCh38">Homo_sapiens GRCh38 hg38</option>
19 1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	21 <option value="GRCh37">Homo_sapiens GRCh37 hg19</option>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	22 <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	23 <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	24 <option value="NCBIM37">Mus_musculus NCBIM37 mm9</option>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	25 <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	26 <option value="user_specified">User specified</option>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	27 </param>
41 74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	28 <when value="GRCh38">
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	29 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	30 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	31 <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	32 <param name="ensembl_version" type="hidden" value="80"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	33 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	34 <param name="ncbi_prefix" type="hidden" value="Hs"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	35 <param name="ucsc_genome_version" type="hidden" value="hg38"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	36 <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"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	37 <param name="mt_chromosome" type="hidden" value="MT"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	38 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	39 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	40 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	41 </when>
19 1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	42 <when value="GRCh37">
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	43 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	44 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	45 <param name="ensembl_genome_version" type="hidden" value="GRCh37"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	46 <param name="ensembl_version" type="hidden" value="71"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	47 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	48 <param name="ncbi_prefix" type="hidden" value="Hs"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	49 <param name="ucsc_genome_version" type="hidden" value="hg19"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	50 <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"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	51 <param name="mt_chromosome" type="hidden" value="MT"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	52 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	53 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	54 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	55 </when>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	56 <when value="NCBI36">
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	57 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	58 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	59 <param name="ensembl_genome_version" type="hidden" value="NCBI36"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	60 <param name="ensembl_version" type="hidden" value="54"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	61 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	62 <param name="ncbi_prefix" type="hidden" value="Hs"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	63 <param name="ucsc_genome_version" type="hidden" value="hg18"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	64 <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"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	65 <param name="mt_chromosome" type="hidden" value="MT"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	66 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	67 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	68 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	69 </when>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	70 <when value="GRCm38">
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	71 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	72 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	73 <param name="ensembl_genome_version" type="hidden" value="GRCm38"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	74 <param name="ensembl_version" type="hidden" value="71"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	75 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	76 <param name="ncbi_prefix" type="hidden" value="Mm"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	77 <param name="ucsc_genome_version" type="hidden" value="mm10"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	78 <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"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	79 <param name="mt_chromosome" type="hidden" value="MT"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	80 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	81 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	82 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	83 </when>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	84 <when value="NCBIM37">
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	85 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	86 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	87 <param name="ensembl_genome_version" type="hidden" value="NCBIM37"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	88 <param name="ensembl_version" type="hidden" value="67"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	89 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	90 <param name="ncbi_prefix" type="hidden" value="Mm"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	91 <param name="ucsc_genome_version" type="hidden" value="mm9"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	92 <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"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	93 <param name="mt_chromosome" type="hidden" value="MT"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	94 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	95 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	96 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	97 </when>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	98 <when value="Rnor_5.0">
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	99 <param name="ensembl_organism" type="hidden" value="rattus_norvegicus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	100 <param name="ensembl_prefix" type="hidden" value="Rattus_norvegicus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	101 <param name="ensembl_genome_version" type="hidden" value="Rnor_5.0"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	102 <param name="ensembl_version" type="hidden" value="71"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	103 <param name="ncbi_organism" type="hidden" value="Rattus_norvegicus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	104 <param name="ncbi_prefix" type="hidden" value="Rn"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	105 <param name="ucsc_genome_version" type="hidden" value="rn5"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	106 <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"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	107 <param name="mt_chromosome" type="hidden" value="MT"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	108 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	109 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	110 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	111 </when>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	112 <when value="user_specified">
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	113 <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name" help="Examples: homo_sapiens, mus_musculus, rattus_norvegicus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	114 <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	115 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	116 <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	117 <param name="ncbi_organism" type="text" value="" label="NCBI Organism Name" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	118 <param name="ncbi_prefix" type="text" value="" label="NCBI Organism Unigene prefix" help="Examples: Hs, Mm, Rn"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	119 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg19, mm10, rn5"/>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	120 <param name="chromosomes" type="text" value="" label="Chromosomes for Ensembl genome build" >
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	121 <help> Examples:
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	122 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
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	123 Mus_musculus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	124 Rattus_norvegicus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,MT
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	125 ( ftp://ftp.ensembl.org/pub/release-71/fasta/homo_sapiens/dna/ )
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	126 </help>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	127 </param>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	128 <param name="mt_chromosome" type="text" value="MT" label="Ensembl Mitochonrial Chromosome name" />
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	129 <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" />
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	130 <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" />
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	131 <param name="rrna_gene_sources" type="text" value="Mt_rRNA,rRNA,rRNA_pseudogene" label="Ribosomal Gene sources" />
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	132 </when>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	133 </conditional>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	134 </inputs>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	135 <outputs>
22 68494d6aabeb Update datamanager and defuse.xml config file generation Jim Johnson <jj@umn.edu> parents: 19 diff changeset	136 <data name="out_file" format="data_manager_json" label="${tool.name} : ${genome.ensembl_genome_version}"/>
19 1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	137 </outputs>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	138 <stdio>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	139 <exit_code range="1:" level="fatal" description="Error running Create DeFuse Reference" />
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	140 <regex match="Error:"
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	141 source="both"
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	142 level="fatal"
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	143 description="Error running Create DeFuse Reference" />
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	144
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	145 </stdio>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	146 <configfiles>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	147 <configfile name="defuse_config">
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	148 #
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	149 # Configuration file for defuse
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	150 #
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	151 # Variables that desiganate the PATH to an application, e.g. __SAMTOOLS_BIN__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	152 # will be set by the runtime script using the ENV PATH
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	153 #
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	154
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	155 # Directory where the defuse code was unpacked
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	156 source_directory = __DEFUSE_PATH__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	157
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	158 # Organism IDs
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	159 ensembl_organism = $genome.ensembl_organism
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	160 ensembl_prefix = $genome.ensembl_prefix
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	161 ensembl_version = $genome.ensembl_version
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	162 ensembl_genome_version = $genome.ensembl_genome_version
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	163 ucsc_genome_version = $genome.ucsc_genome_version
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	164 ncbi_organism = $genome.ncbi_organism
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	165 ncbi_prefix = $genome.ncbi_prefix
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	166
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	167 # Directory where you want your dataset
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	168 dataset_directory = __DATASET_DIRECTORY__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	169
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	170 #raw
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	171 # Input genome and gene models
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	172 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	173 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	174
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	175 # Repeat table from ucsc genome browser
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	176 repeats_filename = $(dataset_directory)/repeats.txt
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	177
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	178 # EST info downloaded from ucsc genome browser
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	179 est_fasta = $(dataset_directory)/est.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	180 est_alignments = $(dataset_directory)/intronEst.txt
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	181
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	182 # Unigene clusters downloaded from ncbi
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	183 unigene_fasta = $(dataset_directory)/$(ncbi_prefix).seq.uniq
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	184 #end raw
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	185
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	186 # Paths to external tools
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	187 samtools_bin = __SAMTOOLS_BIN__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	188 bowtie_bin = __BOWTIE_BIN__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	189 bowtie_build_bin = __BOWTIE_BUILD_BIN__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	190 blat_bin = __BLAT_BIN__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	191 fatotwobit_bin = __FATOTWOBIT_BIN__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	192 gmap_bin = __GMAP_BIN__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	193 gmap_setup_bin = __GMAP_SETUP_BIN__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	194 r_bin = __R_BIN__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	195 rscript_bin = __RSCRIPT_BIN__
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	196
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	197 #raw
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	198 # Directory where you want your dataset
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	199 gmap_index_directory = $(dataset_directory)/gmap
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	200 #end raw
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	201
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	202 #raw
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	203 # Dataset files
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	204 dataset_prefix = $(dataset_directory)/defuse
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	205 chromosome_prefix = $(dataset_prefix).dna.chromosomes
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	206 exons_fasta = $(dataset_prefix).exons.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	207 cds_fasta = $(dataset_prefix).cds.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	208 cdna_regions = $(dataset_prefix).cdna.regions
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	209 cdna_fasta = $(dataset_prefix).cdna.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	210 reference_fasta = $(dataset_prefix).reference.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	211 rrna_fasta = $(dataset_prefix).rrna.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	212 ig_gene_list = $(dataset_prefix).ig.gene.list
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	213 repeats_regions = $(dataset_directory)/repeats.regions
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	214 est_split_fasta1 = $(dataset_directory)/est.1.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	215 est_split_fasta2 = $(dataset_directory)/est.2.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	216 est_split_fasta3 = $(dataset_directory)/est.3.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	217 est_split_fasta4 = $(dataset_directory)/est.4.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	218 est_split_fasta5 = $(dataset_directory)/est.5.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	219 est_split_fasta6 = $(dataset_directory)/est.6.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	220 est_split_fasta7 = $(dataset_directory)/est.7.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	221 est_split_fasta8 = $(dataset_directory)/est.8.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	222 est_split_fasta9 = $(dataset_directory)/est.9.fa
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	223
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	224 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	225 prefilter1 = $(unigene_fasta)
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	226
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	227 # deFuse scripts and tools
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	228 scripts_directory = $(source_directory)/scripts
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	229 tools_directory = $(source_directory)/tools
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	230 data_directory = $(source_directory)/data
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	231 #end raw
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	232
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	233 # Parameters for building the dataset
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	234 chromosomes = $genome.chromosomes
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	235 mt_chromosome = $genome.mt_chromosome
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	236 gene_sources = $genome.gene_sources
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	237 ig_gene_sources = $genome.ig_gene_sources
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	238 rrna_gene_sources = $genome.rrna_gene_sources
41 74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	239 gene_biotypes = $genome.gene_sources
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	240 ig_gene_biotypes = $genome.ig_gene_sources
74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	241 rrna_gene_biotypes = $genome.rrna_gene_sources
19 1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	242
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	243 #raw
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	244 # Remove temp files
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	245 remove_job_files = yes
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	246 remove_job_temp_files = yes
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	247 #end raw
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	248 </configfile>
41 74de1ccc51db Add GRCh38 hg38, minor fixes. Jim Johnson <jj@umn.edu> parents: 22 diff changeset	249 <configfile name="defuse_script">#slurp
19 1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	250 #!/bin/bash
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	251 ## define some things for cheetah proccessing
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	252 #set $amp = chr(38)
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	253 #set $gt = chr(62)
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	254 ## substitute pathnames into config file
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	255 if `grep __DATASET_DIRECTORY__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DATASET_DIRECTORY__#\$1#" $defuse_config; fi
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	256 if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	257 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
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	258 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
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	259 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
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	260 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
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	261 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
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	262 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
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	263 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
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	264 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
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	265 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
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	266 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
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	267 ## copy config to output
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	268 cp $defuse_config \$1/defuse_config.txt
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	269 ## Run the create_reference_dataset.pl
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	270 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	271 </configfile>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	272 </configfiles>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	273
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	274 <tests>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	275 </tests>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	276 <help>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	277 DeFuse
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	278
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	279 DeFuse_ is a software package for gene fusion discovery using RNA-Seq data. The software uses clusters of discordant paired end alignments to inform a split read alignment analysis for finding fusion boundaries. The software also employs a number of heuristic filters in an attempt to reduce the number of false positives and produces a fully annotated output for each predicted fusion. See the DeFuse_Version_0.6_ manual for details.
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	280
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	281 DeFuse uses a Reference Dataset to search for gene fusions. The Reference Dataset is generated from the following sources in DeFuse_Version_0.6_:
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	282 - genome_fasta from Ensembl
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	283 - gene_models from Ensembl
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	284 - repeats_filename from UCSC RepeatMasker rmsk.txt
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	285 - est_fasta from UCSC
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	286 - est_alignments from UCSC intronEst.txt
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	287 - unigene_fasta from NCBI
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	288
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	289 The create_defuse_reference Galaxy tool downloads the reference genome and other source files, and builds any derivative files including bowtie indices, gmap indices, and 2bit files. Expect this step to take at least 12 hours.
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	290
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	291
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	292 It will generate the refernce data for deFuse Galaxy tool.
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	293
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	294 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	295
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	296 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	297
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	298 .. _DeFuse_Version_0.6: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	299
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	300 ------
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	301
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	302 Outputs
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	303
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	304 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths.
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	305
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	306 </help>
1af6f32ff592 Add datamanager, move to defuse_reference.loc Jim Johnson <jj@umn.edu> parents: diff changeset	307 </tool>

Mercurial > repos > jjohnson > defuse

annotate datamanager_create_reference.xml @ 41:74de1ccc51db