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annotate tool-data/fasta_indexes.loc.sample @ 14:b61f5d6a7f25 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_mpileup commit cd62639660bef041ba14ecff337fb98e84e75d8a
author iuc
date Mon, 20 Nov 2023 22:16:18 +0000
parents 5ace23a993fd
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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1 #This is a sample file distributed with Galaxy that enables tools
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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2 #to use a directory of Samtools indexed sequences data files. You will need
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5ace23a993fd Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents: 1
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3 #to create these data files and then create a fasta_indexes.loc file
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dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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4 #similar to this one (store it in this directory) that points to
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5ace23a993fd Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents: 1
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5 #the directories in which those files are stored. The fasta_indexes.loc
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dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
6 #file has this format (white space characters are TAB characters):
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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7 #
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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9 #
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
10 #So, for example, if you had hg19 Canonical indexed stored in
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
11 #
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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12 # /depot/data2/galaxy/hg19/sam/,
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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13 #
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5ace23a993fd Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents: 1
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14 #then the fasta_indexes.loc entry would look like this:
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dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
15 #
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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17 #
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
18 #and your /depot/data2/galaxy/hg19/sam/ directory
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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19 #would contain hg19canon.fa and hg19canon.fa.fai files.
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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20 #
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5ace23a993fd Replace sam_fa_indices.loc with fasta_indexes.loc in fasta_indexes.loc.sample.
devteam
parents: 1
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21 #Your fasta_indexes.loc file should include an entry per line for
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dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
22 #each index set you have stored. The file in the path does actually
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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23 #exist, but it should never be directly used. Instead, the name serves
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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24 #as a prefix for the index file. For example:
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
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25 #
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
dddde948c3e5 Update samtools_mpileup to use the fasta_indexes data table.
Dave Bouvier <dave@bx.psu.edu>
parents:
diff changeset
29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa