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annotate tool-data/liftOver.loc.sample @ 30:179bf64d12ef draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 3cceec514024bda448f7b8f207b09e49cba63de1-dirty
author yhoogstrate
date Thu, 12 Nov 2015 10:26:25 -0500
parents cb854f5d6a4b
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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7
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
1 #This is a sample file distributed with Galaxy that is used by the
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
2 #liftOver tools. The liftOver.loc file has this format (white space
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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3 #characters are TAB characters):
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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4 #
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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5 #<FromSpecies> <ToSpecies> <PathToChainFile>
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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6 #
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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7 #So, for example, if you had the chain file to convert from anoCar1 to galGal3
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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8 #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain,
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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9 #then the liftOver.loc entry would look like this:
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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10 #
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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11 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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12 #
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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13 #and your /depot/data2/galaxy/anoCar1/liftOver directory would
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
diff changeset
14 #contain all of your "chain" files (e.g.):
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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15 #
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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16 #-rw-rw-r-- 1 gua110 galaxy 24046079 2008-01-16 14:20 anoCar1ToGalGal3.over.chain
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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17 #-rw-rw-r-- 1 gua110 galaxy 13216668 2008-01-16 14:20 anoCar1ToGasAcu1.over.chain
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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18 #-rw-rw-r-- 1 gua110 galaxy 29597067 2008-01-16 14:20 anoCar1ToHg18.over.chain
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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19 #...etc...
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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20 #
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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21 #Your liftOver.loc file should include an entry per line for each build you can
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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22 #convert. For example:
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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23 #
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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24 #anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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25 #anoCar1 gasAcu1 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGasAcu1.over.chain
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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26 #anoCar1 hg18 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToHg18.over.chain
cb854f5d6a4b planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 8f9242188a8e8e942af6625014a959e70dcb896a
yhoogstrate
parents:
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27 #...etc...