Mercurial > repos > iuc > jcvi_gff_stats

annotate tool-data/all_fasta.loc.sample @ 1:8cffbd184762 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit 69b89d1e8d108e91c81099e5f922357183dc2490
author iuc
date Thu, 02 Aug 2018 12:31:05 -0400
parents 2defe48e4c7a
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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1 #This file lists the locations and dbkeys of all the fasta files
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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2 #under the "genome" directory (a directory that contains a directory
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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3 #for each build). The script extract_fasta.py will generate the file
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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4 #all_fasta.loc. This file has the format (white space characters are
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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5 #TAB characters):
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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diff changeset
6 #
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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8 #
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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9 #So, all_fasta.loc could look something like this:
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
parents:
diff changeset
10 #
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
parents:
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
parents:
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14 #
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
parents:
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16 #fasta file. So there will be multiple fasta files for each build,
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
parents:
diff changeset
17 #such as with hg19 above.
2defe48e4c7a planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jcvi_gff_stats commit f1e2c895bec4b8bf960d54f634c69fe18411846a
iuc
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18 #