annotate tool-data/all_fasta.loc.sample @ 17:e0de8669b340 draft default tip

planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit 39442b43654a912285459264a7aad1f19e00940a
author richard-burhans
date Mon, 18 Nov 2024 17:24:04 +0000
parents bf80a7ed8595
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
5
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
1 #This file lists the locations and dbkeys of all the fasta files
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
2 #under the "genome" directory (a directory that contains a directory
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
3 #for each build). The script extract_fasta.py will generate the file
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
4 #all_fasta.loc. This file has the format (white space characters are
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
5 #TAB characters):
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
6 #
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
7 #<unique_build_id> <dbkey> <display_name> <file_path>
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
8 #
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
9 #So, all_fasta.loc could look something like this:
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
10 #
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
14 #
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
15 #Your all_fasta.loc file should contain an entry for each individual
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
16 #fasta file. So there will be multiple fasta files for each build,
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
17 #such as with hg19 above.
bf80a7ed8595 planemo upload for repository https://github.com/richard-burhans/galaxytools/tree/main/tools/ncbi_egapx commit bbb1a61647b7a3e5297f2cbd09f55dff169a428f
richard-burhans
parents:
diff changeset
18 #