Mercurial > repos > iuc > homer_gtf_to_annotations

annotate tool-data/homer_preparse.loc.sample @ 1:debfd2838aca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit a03582e72f78a25fb4d840a1ec0cb4ef61473bb9"
author iuc
date Sun, 26 Sep 2021 12:28:29 +0000
parents 8ebb6520eef4
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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1 # homer_preparse.loc.sample
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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2 # This is a *.loc.sample file distributed with Galaxy that enables tools
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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3 # to use a directory of indexed data files. This one is for Homer preparsed genomes.
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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4 # The file should include an one line entry for each index set.
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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5 # The path points to the "directory" for the set, not a specific file.
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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6 # It has six text columns seperated by TABS.
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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7 #
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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8 # <unique_preparse_id> <dbkey> <mask> <size> <display_name> <directory_path> <path_fasta> <version>
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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9 #
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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10 # So, for example, if you had phiX174 preparsed with 200bp stored in:
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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11 #
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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12 # /tmp/phix_200
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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13 #
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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14 # containing phiX174.fasta.200.* files, such as:
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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15 # -rw-r--r-- 1 ldelisle ldelisle 83K Jul 9 10:14 phiX174.fasta.200.cgbins
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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16 # -rw-r--r-- 1 ldelisle ldelisle 249K Jul 9 10:14 phiX174.fasta.200.cgfreq
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
iuc
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17 # -rw-r--r-- 1 ldelisle ldelisle 83K Jul 9 10:14 phiX174.fasta.200.gcbins
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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18 # -rw-r--r-- 1 ldelisle ldelisle 169K Jul 9 10:14 phiX174.fasta.200.pos
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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19 # -rw-r--r-- 1 ldelisle ldelisle 955K Jul 9 10:14 phiX174.fasta.200.seq
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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20 #
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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21 # then the homer_preparse.loc entry could look like this:
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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22 #
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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23 # phiX174_200 phiX174 False 200 phiX174 (200bp) /tmp/phix_200 /tmp/phiX174.fasta 4.11
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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24 #
8ebb6520eef4 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/homer commit e49d856e0181edc6120220a1b819cba2466a4289"
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25 #