annotate test-data/fasta_indexes.loc @ 1:5a2cb67ef742 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit bced16a45d19b243a244a093c3b3504b2640d5e0
author iuc
date Mon, 22 Apr 2024 17:46:31 +0000
parents ef9a50eb20ce
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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1 #This is a sample file distributed with Galaxy that enables tools
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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2 #to use a directory of Samtools indexed sequences data files. You will need
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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3 #to create these data files and then create a fasta_indexes.loc file
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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4 #similar to this one (store it in this directory) that points to
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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5 #the directories in which those files are stored. The fasta_indexes.loc
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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6 #file has this format (white space characters are TAB characters):
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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7 #
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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9 #
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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10 #So, for example, if you had hg19 Canonical indexed stored in
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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11 #
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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12 # /depot/data2/galaxy/hg19/sam/,
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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13 #
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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14 #then the fasta_indexes.loc entry would look like this:
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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15 #
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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17 #
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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18 #and your /depot/data2/galaxy/hg19/sam/ directory
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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19 #would contain hg19canon.fa and hg19canon.fa.fai files.
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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20 #
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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21 #Your fasta_indexes.loc file should include an entry per line for
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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22 #each index set you have stored. The file in the path does actually
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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23 #exist, but it should never be directly used. Instead, the name serves
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
iuc
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24 #as a prefix for the index file. For example:
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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25 #
ef9a50eb20ce planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/cnvkit commit e927b17a345b18c1b51dc1b112db5129278dcd22
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26 test_buildid hg17 test_displayname ${__HERE__}/genome.fasta