Mercurial > repos > rnateam > paralyzer

annotate tool-data/lastz_seqs.loc.sample @ 0:d4d72f60e8d6 draft default tip

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
author rnateam
date Wed, 23 Oct 2019 19:07:59 -0400
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d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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1 #This is a sample file distributed with Galaxy that enables tools
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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2 #to use a directory of 2bit genome files for use with Lastz. You will
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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3 #need to supply these files and then create a lastz_seqs.loc file
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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4 #similar to this one (store it in this directory) that points to
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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5 #the directories in which those files are stored. The lastz_seqs.loc
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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6 #file has this format (white space characters are TAB characters):
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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7 #
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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8 #<unique_build_id> <display_name> <file_path>
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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9 #
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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10 #So, for example, if your lastz_seqs.loc began like this:
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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11 #
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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12 #hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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13 #hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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14 #mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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15 #
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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16 #then your /depot/data2/galaxy/twobit/ directory
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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17 #would need to contain the following 2bit files:
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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18 #
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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22 #
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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23 #Your lastz_seqs.loc file should include an entry per line for
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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24 #each file you have stored that you want to be available. Note that
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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25 #your files should all have the extension '2bit'.
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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26 #
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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27 #Note that for backwards compatibility with workflows, the unique ID of
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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28 #an entry must be the path that was in the original loc file, because that
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
rnateam
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29 #is the value stored in the workflow for that parameter.
d4d72f60e8d6 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/paralyzer commit d0cc3dca3aafecf306a0bfb0cd1268b4d5b3e244"
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30 #