Mercurial > repos > rhpvorderman > data_manager_select_index_by_path

comparison data_manager/indexes.yml @ 1:8495c49cd056 draft default tip

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planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 9061997af3bc94f49653ffd42f10b973578e371d
author rhpvorderman
date Mon, 16 Jul 2018 10:58:36 -0400
parents 5f8d9309058b
children
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0:5f8d9309058b 1:8495c49cd056
1 ---
2 # This file contains information about all the indexes.
3 #
4 # Top keys are table names as used in Galaxy.
5 # These names can be viewed in the 'local data' part of the admin menu
6 #
7 # Keys for each table
8 # name:
9 # (STRING) The name of the index.
10 # This is used for error reporting in the program
11 #
12 # prefix:
13 # (BOOLEAN) whether the index is a prefix. For example
14 # for bwa_mem-indexes, the index path is 'reference.fa'.
15 # This is a prefix because all the reference files are:
16 # 'reference.fa.amb', 'reference.fa.ann' etc.
17 #
18 # prefix_strip_extension:
19 # (BOOLEAN) whether the prefix should be stripped
20 # of its extensions. Ie from 'reference.fa' to
21 # 'reference'. For a picard index also a 'reference.dict'
22 # should be present, so the prefix needs to be stripped of
23 # its extension to look for the index files.
24 #
25 # extensions:
26 # (LIST[STRING]) a list of strings with the extensions:
27 # for example:
28 # extensions:
29 # - .fai
30 #
31 # folder:
32 # (LIST[STRING]) Use this when the index is not a prefix but a folder
33 # the program will check if all the files in the list are present.
34 # If they are not, an exception will follow.
35 #
36 # extra_columns:
37 # (LIST[STRING]) Usual indexes have 4 columns in the data table: path, name,
38 # value, dbkey. But some indexes have additional columns. rnastar_index2
39 # needs a 'with-gtf' column for instance. Add these columns to the list to
40 # make sure their presence, or non-presence is checked.
41
1 all_fasta: 42 all_fasta:
2 name: fasta file 43 name: fasta file
3 extensions: 44 prefix: false
4 - .fa 45
5 no_prefix: True
6 bowtie2_indexes: 46 bowtie2_indexes:
7 name: bowtie2 index 47 name: bowtie2 index
8 extensions: 48 extensions:
9 - .bt2 49 - .bt2
50
10 bowtie_indexes: 51 bowtie_indexes:
11 name: bowtie index 52 name: bowtie index
12 extensions: 53 extensions:
13 - .ebwt 54 - .ebwt
55
14 bowtie_indexes_color: 56 bowtie_indexes_color:
15 name: bowtie color index 57 name: bowtie color index
16 extensions: 58 extensions:
17 - .ebwt 59 - .ebwt
60
18 bwa_mem_indexes: 61 bwa_mem_indexes:
19 name: bwa mem index 62 name: bwa mem index
20 extensions: 63 extensions:
21 - .amb 64 - .amb
22 - .ann 65 - .ann
23 - .bwt 66 - .bwt
24 - .pac 67 - .pac
25 - .sa 68 - .sa
69
26 bwameth_indexes: 70 bwameth_indexes:
27 name: bwa_meth_index 71 name: bwa_meth_index
28 fasta_indexes: 72 fasta_indexes:
29 name: fasta index 73 name: fasta index
30 extensions: 74 extensions:
31 - .fai 75 - .fai
76
32 gatk_picard_index: 77 gatk_picard_index:
33 name: picard index for GATK 78 name: picard index for GATK
79
34 gene_transfer: 80 gene_transfer:
35 name: Gene Transfer File 81 name: Gene Transfer File
36 extensions: 82 extensions:
37 - .gtf 83 - .gtf
84
38 hisat2_indexes: 85 hisat2_indexes:
39 name: hisat2 index 86 name: hisat2 index
40 extensions: 87 extensions:
41 - .ht2 88 - .ht2
89
42 kallisto_indexes: 90 kallisto_indexes:
43 name: kallisto index 91 name: kallisto index
44 no_prefix: True 92 prefix: false
93
45 picard_indexes: 94 picard_indexes:
46 name: picard index 95 name: picard index
96 prefix_strip_extension: true
97 extensions:
98 - ".fa"
99 - ".dict"
100
101 rnastar_index2:
102 name: "Star index"
103 prefix: false
104 extra_columns:
105 - with-gtf
106 folder:
107 - chrLength.txt
108 - chrNameLength.txt
109 - chrStart.txt
110 - chrName.txt
111 - Genome
112 - SA
113 - SAindex
114 - genomeParameters.txt
115
47 tophat2_indexes: 116 tophat2_indexes:
48 name: tophat2 index 117 name: tophat2 index
49 extensions: 118 extensions:
50 - .bt2 119 - .bt2