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annotate tool-data/all_fasta.loc.sample @ 6:8694fa7c8b78 draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Wed, 01 Sep 2021 08:35:18 +0000
parents 57baf87c7fcd
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
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1 #This file lists the locations and dbkeys of all the genome and transcriptome fasta files
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
3 #for each build. This file has the format (white space characters are
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
4 #TAB characters):
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
5 #
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
6 #<unique_build_id> <dbkey> <display_name> <file_path>
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
7 #
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
8 #So, all_fasta.loc could look something like this:
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
9 #
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
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10 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
11 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
12 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
13 #hg19full.87 hg19 Human (Homo sapiens): hg19 Full Trans v87 /path/to/genome/hg19/hg19full.cdna.all.fa
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
14
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
parents:
diff changeset
17 #such as with hg19 above.
57baf87c7fcd planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scpipe commit 8908da9cdd112ae0943dbf1eccb221e84cd99ca7
iuc
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18 #