Mercurial > repos > jjohnson > defuse

annotate create_reference_dataset.xml @ 11:b22f8634ff84 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
author jjohnson
date Sun, 17 Jan 2016 14:11:06 -0500
parents
children b67c24d902aa
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
1 <tool id="create_defuse_reference" name="Create DeFuse Reference" version="@DEFUSE_VERSION@.1">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
2 <description>create a defuse reference from Ensembl and UCSC sources</description>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
3 <macros>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
4 <import>macros.xml</import>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
5 </macros>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
6 <requirements>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
7 <expand macro="defuse_requirement" />
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
8 <expand macro="mapping_requirements" />
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
9 </requirements>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
10 <command interpreter="command"> /bin/bash $defuse_script </command>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
11 <inputs>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
12 <conditional name="genome">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
13 <param name="choice" type="select" label="Select a Genome Build">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
14 <option value="GRCh38">Homo_sapiens GRCh38 hg38</option>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
15 <option value="GRCh37">Homo_sapiens GRCh37 hg19</option>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
16 <option value="NCBI36">Homo_sapiens NCBI36 hg18</option>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
17 <option value="GRCm38">Mus_musculus GRCm38 mm10</option>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
18 <option value="NCBIM37">Mus_musculus NCBIM37 mm9</option>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
19 <option value="Rnor_5.0">Rattus_norvegicus Rnor_5.0 rn5</option>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
20 <option value="user_specified">User specified</option>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
21 </param>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
22 <when value="GRCh38">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
23 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
24 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
25 <param name="ensembl_genome_version" type="hidden" value="GRCh38"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
26 <param name="ensembl_version" type="hidden" value="80"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
27 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
28 <param name="ncbi_prefix" type="hidden" value="Hs"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
29 <param name="ucsc_genome_version" type="hidden" value="hg38"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
30 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
31 <param name="mt_chromosome" type="hidden" value="MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
32 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
33 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
34 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
35 </when>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
36 <when value="GRCh37">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
37 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
38 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
39 <param name="ensembl_genome_version" type="hidden" value="GRCh37"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
40 <param name="ensembl_version" type="hidden" value="71"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
41 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
42 <param name="ncbi_prefix" type="hidden" value="Hs"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
43 <param name="ucsc_genome_version" type="hidden" value="hg19"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
44 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
45 <param name="mt_chromosome" type="hidden" value="MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
46 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
47 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
48 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
49 </when>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
50 <when value="NCBI36">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
51 <param name="ensembl_organism" type="hidden" value="homo_sapiens"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
52 <param name="ensembl_prefix" type="hidden" value="Homo_sapiens"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
53 <param name="ensembl_genome_version" type="hidden" value="NCBI36"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
54 <param name="ensembl_version" type="hidden" value="54"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
55 <param name="ncbi_organism" type="hidden" value="Homo_sapiens"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
56 <param name="ncbi_prefix" type="hidden" value="Hs"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
57 <param name="ucsc_genome_version" type="hidden" value="hg18"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
58 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
59 <param name="mt_chromosome" type="hidden" value="MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
60 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
61 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
62 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
63 </when>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
64 <when value="GRCm38">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
65 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
66 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
67 <param name="ensembl_genome_version" type="hidden" value="GRCm38"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
68 <param name="ensembl_version" type="hidden" value="71"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
69 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
70 <param name="ncbi_prefix" type="hidden" value="Mm"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
71 <param name="ucsc_genome_version" type="hidden" value="mm10"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
72 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
73 <param name="mt_chromosome" type="hidden" value="MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
74 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
75 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
76 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
77 </when>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
78 <when value="NCBIM37">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
79 <param name="ensembl_organism" type="hidden" value="mus_musculus"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
80 <param name="ensembl_prefix" type="hidden" value="Mus_musculus"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
81 <param name="ensembl_genome_version" type="hidden" value="NCBIM37"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
82 <param name="ensembl_version" type="hidden" value="67"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
83 <param name="ncbi_organism" type="hidden" value="Mus_musculus"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
84 <param name="ncbi_prefix" type="hidden" value="Mm"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
85 <param name="ucsc_genome_version" type="hidden" value="mm9"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
86 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
87 <param name="mt_chromosome" type="hidden" value="MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
88 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
89 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
90 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
91 </when>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
92 <when value="Rnor_5.0">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
93 <param name="ensembl_organism" type="hidden" value="rattus_norvegicus"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
94 <param name="ensembl_prefix" type="hidden" value="Rattus_norvegicus"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
95 <param name="ensembl_genome_version" type="hidden" value="Rnor_5.0"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
96 <param name="ensembl_version" type="hidden" value="71"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
97 <param name="ncbi_organism" type="hidden" value="Rattus_norvegicus"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
98 <param name="ncbi_prefix" type="hidden" value="Rn"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
99 <param name="ucsc_genome_version" type="hidden" value="rn5"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
100 <param name="chromosomes" type="hidden" value="1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
101 <param name="mt_chromosome" type="hidden" value="MT"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
102 <param name="gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
103 <param name="ig_gene_sources" type="hidden" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
104 <param name="rrna_gene_sources" type="hidden" value="Mt_rRNA,rRNA,rRNA_pseudogene"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
105 </when>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
106 <when value="user_specified">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
107 <param name="ensembl_organism" type="text" value="" label="Ensembl Organism Name">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
108 <help>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
109 Examples: homo_sapiens, mus_musculus, rattus_norvegicus
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
110 ftp://ftp.ensembl.org/pub/release-$ensembl_version/fasta/$ensembl_organism/dna/$ensembl_prefix.$ensembl_genome_version.$ensembl_version.dna.chromosome.$chromosome.fa.gz
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
111 </help>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
112 </param>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
113 <param name="ensembl_prefix" type="text" value="" label="Ensembl Organism prefix" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
114 <param name="ensembl_genome_version" type="text" value="" label="Ensembl Genome Version" help="Examples: GRCh37, GRCm38, Rnor_5.0"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
115 <param name="ensembl_version" type="integer" value="" label="Ensembl Release Version" help="Example: 71"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
116 <param name="ncbi_organism" type="text" value="" label="NCBI Organism Name" help="Examples: Homo_sapiens, Mus_musculus, Rattus_norvegicus"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
117 <param name="ncbi_prefix" type="text" value="" label="NCBI Organism Unigene prefix" help="Examples: Hs, Mm, Rn"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
118 <param name="ucsc_genome_version" type="text" value="" label="UCSC Genome Version" help="Examples: hg19, mm10, rn5"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
119 <param name="chromosomes" type="text" value="" label="Chromosomes for Ensembl genome build" >
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
120 <help> Examples:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
121 Homo_sapiens: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y,MT
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
122 Mus_musculus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,Y,MT
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
123 Rattus_norvegicus: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,X,MT
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
124 ( ftp://ftp.ensembl.org/pub/release-71/fasta/homo_sapiens/dna/ )
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
125 </help>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
126 </param>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
127 <param name="mt_chromosome" type="text" value="MT" label="Ensembl Mitochonrial Chromosome name" />
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
128 <param name="gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,processed_transcript,protein_coding" label="Gene sources" />
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
129 <param name="ig_gene_sources" type="text" value="IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,IG_pseudogene" label="IG Gene sources" />
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
130 <param name="rrna_gene_sources" type="text" value="Mt_rRNA,rRNA,rRNA_pseudogene" label="Ribosomal Gene sources" />
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
131 </when>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
132 </conditional>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
133 </inputs>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
134 <outputs>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
135 <data format="defuse.conf" name="config_txt" label="${tool.name} on ${genome.ensembl_genome_version} : config.txt"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
136 </outputs>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
137 <stdio>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
138 <exit_code range="1:" level="fatal" description="Error running Create DeFuse Reference" />
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
139 <regex match="Error:"
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
140 source="both"
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
141 level="fatal"
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
142 description="Error running Create DeFuse Reference" />
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
143
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
144 </stdio>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
145 <configfiles>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
146 <configfile name="defuse_config">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
147 #
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
148 # Configuration file for defuse
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
149 #
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
150 # Variables that desiganate the PATH to an application, e.g. __SAMTOOLS_BIN__
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
151 # will be set by the runtime script using the ENV PATH
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
152 #
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
153
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
154 # Directory where the defuse code was unpacked
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
155 source_directory = __DEFUSE_PATH__
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
156
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
157 # Organism IDs
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
158 ensembl_organism = $genome.ensembl_organism
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
159 ensembl_prefix = $genome.ensembl_prefix
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
160 ensembl_version = $genome.ensembl_version
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
161 ensembl_genome_version = $genome.ensembl_genome_version
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
162 ucsc_genome_version = $genome.ucsc_genome_version
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
163 ncbi_organism = $genome.ncbi_organism
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
164 ncbi_prefix = $genome.ncbi_prefix
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
165
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
166 # Directory where you want your dataset
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
167 dataset_directory = $config_txt.dataset.extra_files_path
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
168
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
169 #raw
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
170 # Input genome and gene models
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
171 gene_models = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).gtf
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
172 genome_fasta = $(dataset_directory)/$(ensembl_prefix).$(ensembl_genome_version).$(ensembl_version).dna.chromosomes.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
173
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
174 # Repeat table from ucsc genome browser
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
175 repeats_filename = $(dataset_directory)/repeats.txt
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
176
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
177 # EST info downloaded from ucsc genome browser
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
178 est_fasta = $(dataset_directory)/est.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
179 est_alignments = $(dataset_directory)/intronEst.txt
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
180
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
181 # Unigene clusters downloaded from ncbi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
182 unigene_fasta = $(dataset_directory)/$(ncbi_prefix).seq.uniq
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
183 #end raw
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
184
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
185 # Paths to external tools
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
186 samtools_bin = __SAMTOOLS_BIN__
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
187 bowtie_bin = __BOWTIE_BIN__
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
188 bowtie_build_bin = __BOWTIE_BUILD_BIN__
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
189 blat_bin = __BLAT_BIN__
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
190 fatotwobit_bin = __FATOTWOBIT_BIN__
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
191 gmap_bin = __GMAP_BIN__
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
192 gmap_setup_bin = __GMAP_SETUP_BIN__
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
193 r_bin = __R_BIN__
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
194 rscript_bin = __RSCRIPT_BIN__
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
195
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
196 #raw
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
197 # Directory where you want your dataset
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
198 gmap_index_directory = $(dataset_directory)/gmap
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
199 #end raw
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
200
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
201 #raw
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
202 # Dataset files
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
203 dataset_prefix = $(dataset_directory)/defuse
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
204 chromosome_prefix = $(dataset_prefix).dna.chromosomes
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
205 exons_fasta = $(dataset_prefix).exons.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
206 cds_fasta = $(dataset_prefix).cds.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
207 cdna_regions = $(dataset_prefix).cdna.regions
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
208 cdna_fasta = $(dataset_prefix).cdna.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
209 reference_fasta = $(dataset_prefix).reference.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
210 rrna_fasta = $(dataset_prefix).rrna.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
211 ig_gene_list = $(dataset_prefix).ig.gene.list
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
212 repeats_regions = $(dataset_directory)/repeats.regions
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
213 est_split_fasta1 = $(dataset_directory)/est.1.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
214 est_split_fasta2 = $(dataset_directory)/est.2.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
215 est_split_fasta3 = $(dataset_directory)/est.3.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
216 est_split_fasta4 = $(dataset_directory)/est.4.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
217 est_split_fasta5 = $(dataset_directory)/est.5.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
218 est_split_fasta6 = $(dataset_directory)/est.6.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
219 est_split_fasta7 = $(dataset_directory)/est.7.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
220 est_split_fasta8 = $(dataset_directory)/est.8.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
221 est_split_fasta9 = $(dataset_directory)/est.9.fa
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
222
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
223 # Fasta files with bowtie indices for prefiltering reads for concordantly mapping pairs
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
224 prefilter1 = $(unigene_fasta)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
225
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
226 # deFuse scripts and tools
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
227 scripts_directory = $(source_directory)/scripts
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
228 tools_directory = $(source_directory)/tools
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
229 data_directory = $(source_directory)/data
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
230 #end raw
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
231
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
232 # Parameters for building the dataset
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
233 chromosomes = $genome.chromosomes
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
234 mt_chromosome = $genome.mt_chromosome
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
235 gene_sources = $genome.gene_sources
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
236 ig_gene_sources = $genome.ig_gene_sources
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
237 rrna_gene_sources = $genome.rrna_gene_sources
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
238 gene_biotypes = $genome.gene_sources
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
239 ig_gene_biotypes = $genome.ig_gene_sources
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
240 rrna_gene_biotypes = $genome.rrna_gene_sources
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
241
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
242 #raw
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
243 # Remove temp files
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
244 remove_job_files = yes
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
245 remove_job_temp_files = yes
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
246 #end raw
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
247 </configfile>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
248 <configfile name="defuse_script">
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
249 #!/bin/bash
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
250 ## define some things for cheetah proccessing
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
251 #set $amp = chr(38)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
252 #set $gt = chr(62)
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
253 ## substitute pathnames into config file
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
254 if `grep __DEFUSE_PATH__ $defuse_config ${gt} /dev/null`;then sed -i'.tmp' "s#__DEFUSE_PATH__#\${DEFUSE_PATH}#" $defuse_config; fi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
255 if `grep __SAMTOOLS_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} SAMTOOLS_BIN=`which samtools`;then sed -i'.tmp' "s#__SAMTOOLS_BIN__#\${SAMTOOLS_BIN}#" $defuse_config; fi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
256 if `grep __BOWTIE_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BIN=`which bowtie`;then sed -i'.tmp' "s#__BOWTIE_BIN__#\${BOWTIE_BIN}#" $defuse_config; fi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
257 if `grep __BOWTIE_BUILD_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BOWTIE_BUILD_BIN=`which bowtie-build`;then sed -i'.tmp' "s#__BOWTIE_BUILD_BIN__#\${BOWTIE_BUILD_BIN}#" $defuse_config; fi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
258 if `grep __BLAT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} BLAT_BIN=`which blat`;then sed -i'.tmp' "s#__BLAT_BIN__#\${BLAT_BIN}#" $defuse_config; fi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
259 if `grep __FATOTWOBIT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} FATOTWOBIT_BIN=`which faToTwoBit`;then sed -i'.tmp' "s#__FATOTWOBIT_BIN__#\${FATOTWOBIT_BIN}#" $defuse_config; fi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
260 if `grep __GMAP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_BIN=`which gmap`;then sed -i'.tmp' "s#__GMAP_BIN__#\${GMAP_BIN}#" $defuse_config; fi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
261 if `grep __GMAP_SETUP_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_SETUP_BIN=`which gmap_setup`;then sed -i'.tmp' "s#__GMAP_SETUP_BIN__#\${GMAP_SETUP_BIN}#" $defuse_config; fi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
262 if `grep __GMAP_INDEX_DIR__ $defuse_config ${gt} /dev/null` ${amp}${amp} GMAP_INDEX_DIR=`pwd`/gmap;then sed -i'.tmp' "s#__GMAP_INDEX_DIR__#\${GMAP_INDEX_DIR}#" $defuse_config; fi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
263 if `grep __R_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} R_BIN=`which R`;then sed -i'.tmp' "s#__R_BIN__#\${R_BIN}#" $defuse_config; fi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
264 if `grep __RSCRIPT_BIN__ $defuse_config ${gt} /dev/null` ${amp}${amp} RSCRIPT_BIN=`which Rscript`;then sed -i'.tmp' "s#__RSCRIPT_BIN__#\${RSCRIPT_BIN}#" $defuse_config; fi
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
265 ## copy config to output
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
266 cp $defuse_config $config_txt
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
267 ## make a data_dir and ln -s the input fastq
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
268 mkdir -p $config_txt.dataset.extra_files_path
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
269 ## create_reference_dataset.pl
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
270 perl \${DEFUSE_PATH}/scripts/create_reference_dataset.pl -c $defuse_config
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
271 </configfile>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
272 </configfiles>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
273
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
274 <tests>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
275 </tests>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
276 <help>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
277 **DeFuse**
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
278
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
280
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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_:
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
282 - genome_fasta from Ensembl
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
283 - gene_models from Ensembl
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
284 - repeats_filename from UCSC RepeatMasker rmsk.txt
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
285 - est_fasta from UCSC
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
286 - est_alignments from UCSC intronEst.txt
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
287 - unigene_fasta from NCBI
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
288
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
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.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
290
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
291
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
292 It will generate a config.txt file that can be input into the deFuse Galaxy tool.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
293
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
294 Journal reference: http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001138
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
295
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
296 .. _DeFuse: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=Main_Page
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
297
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
298 .. _DeFuse_Version_0.6: http://sourceforge.net/apps/mediawiki/defuse/index.php?title=DeFuse_Version_0.6.1
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
299
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
300 ------
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
301
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
302 **Outputs**
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
303
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
304 The galaxy history will contain: the config.txt file that provides DeFuse with the reference data paths.
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
305
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
306 </help>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
307 <expand macro="citations"/>
b22f8634ff84 planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/defuse commit 23b94b5747c6956360cd2eca0a07a669929ea141-dirty
jjohnson
parents:
diff changeset
308 </tool>