Mercurial > repos > rhpvorderman > data_manager_select_index_by_path

annotate data_manager/indexes.yml @ 39:ad5d85570342 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 a9b8c9549044fb951570d9c6cf88107d98800afb
author rhpvorderman
date Wed, 25 Jul 2018 10:34:49 -0400
parents bfc8a44fce75
children
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0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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parents: 12
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1 ---
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645c33d0786a planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit cb6d569e0496fac22e0e9c7fffa884338cef09c8
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2 # This file contains information about all the indexes.
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0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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3 #
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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4 # Top keys are table names as used in Galaxy.
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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parents: 12
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5 # These names can be viewed in the 'local data' part of the admin menu
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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6 #
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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7 # Keys for each table
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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8 # name:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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9 # (STRING) The name of the index.
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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10 # This is used for error reporting in the program
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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11 #
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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12 # prefix:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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13 # (BOOLEAN) whether the index is a prefix. For example
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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14 # for bwa_mem-indexes, the index path is 'reference.fa'.
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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parents: 12
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15 # This is a prefix because all the reference files are:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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16 # 'reference.fa.amb', 'reference.fa.ann' etc.
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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17 #
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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18 # prefix_strip_extension:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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19 # (BOOLEAN) whether the prefix should be stripped
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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20 # of its extensions. Ie from 'reference.fa' to
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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parents: 12
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21 # 'reference'. For a picard index also a 'reference.dict'
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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22 # should be present, so the prefix needs to be stripped of
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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23 # its extension to look for the index files.
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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24 #
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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25 # extensions:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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26 # (LIST[STRING]) a list of strings with the extensions:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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parents: 12
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27 # for example:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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28 # extensions:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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29 # - .fai
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30 #
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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31 # folder:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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32 # (LIST[STRING]) Use this when the index is not a prefix but a folder
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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33 # the program will check if all the files in the list are present.
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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34 # If they are not, an exception will follow.
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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35 #
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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36 # extra_columns:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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37 # (LIST[STRING]) Usual indexes have 4 columns in the data table: path, name,
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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38 # value, dbkey. But some indexes have additional columns. rnastar_index2
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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39 # needs a 'with-gtf' column for instance. Add these columns to the list to
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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40 # make sure their presence, or non-presence is checked.
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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41
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42 all_fasta:
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43 name: fasta file
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44 prefix: false
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46 bowtie2_indexes:
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47 name: bowtie2 index
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48 extensions:
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49 - .bt2
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51 bowtie_indexes:
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52 name: bowtie index
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53 extensions:
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54 - .ebwt
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56 bowtie_indexes_color:
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57 name: bowtie color index
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58 extensions:
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
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59 - .ebwt
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61 bwa_mem_indexes:
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62 name: bwa mem index
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63 extensions:
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64 - .amb
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
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65 - .ann
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66 - .bwt
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67 - .pac
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68 - .sa
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70 bwameth_indexes:
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71 name: bwa_meth_index
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72 fasta_indexes:
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73 name: fasta index
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74 extensions:
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75 - .fai
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77 gatk_picard_index:
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78 name: picard index for GATK
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80 gene_transfer:
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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diff changeset
81 name: Gene Transfer File
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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diff changeset
82 extensions:
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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diff changeset
83 - .gtf
13
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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84
11
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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diff changeset
85 hisat2_indexes:
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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diff changeset
86 name: hisat2 index
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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diff changeset
87 extensions:
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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diff changeset
88 - .ht2
13
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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89
11
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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diff changeset
90 kallisto_indexes:
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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91 name: kallisto index
13
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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92 prefix: false
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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93
11
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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94 picard_indexes:
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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95 name: picard index
13
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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96 prefix_strip_extension: true
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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diff changeset
97 extensions:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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diff changeset
98 - ".fa"
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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99 - ".dict"
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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100
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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101 rnastar_index2:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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102 name: "Star index"
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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103 prefix: false
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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104 extra_columns:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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105 - with-gtf
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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106 folder:
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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107 - chrLength.txt
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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108 - chrNameLength.txt
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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109 - chrStart.txt
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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110 - chrName.txt
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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111 - Genome
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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112 - SA
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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113 - SAindex
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
rhpvorderman
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114 - genomeParameters.txt
0a1afc109ad9 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 72334942019bfd598086f39ba93d4b4fce3cda19
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115
11
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
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116 tophat2_indexes:
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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117 name: tophat2 index
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
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118 extensions:
8ccfeedd1f03 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit 6fd3421f2405e0e56147f1ee807c297dad8e547d
rhpvorderman
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119 - .bt2
38
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
rhpvorderman
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120
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
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121 centrifuge_indices:
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
rhpvorderman
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122 name: Centrifuge index
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
rhpvorderman
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123 folder: []
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
rhpvorderman
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124 prefix: false
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
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125
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
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126 kraken_databases:
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
rhpvorderman
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127 name: Kraken database
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
rhpvorderman
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128 folder:
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
rhpvorderman
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129 - database.idx
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
rhpvorderman
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130 - database.kdb
bfc8a44fce75 planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit daef12f8aec8822a48689b303cd216ef774f1110
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131 prefix: false