Mercurial > repos > rhpvorderman > data_manager_select_index_by_path

annotate tool-data/fasta_indexes.loc.sample @ 0:5f8d9309058b draft

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planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
author rhpvorderman
date Mon, 25 Sep 2017 03:35:26 -0400
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5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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1 #This is a sample file distributed with Galaxy that enables tools
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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2 #to use a directory of Samtools indexed sequences data files. You will need
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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3 #to create these data files and then create a fasta_indexes.loc file
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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4 #similar to this one (store it in this directory) that points to
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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5 #the directories in which those files are stored. The fasta_indexes.loc
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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6 #file has this format (white space characters are TAB characters):
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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7 #
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path>
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff changeset
9 #
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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10 #So, for example, if you had hg19 Canonical indexed stored in
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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11 #
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
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12 # /depot/data2/galaxy/hg19/sam/,
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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13 #
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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14 #then the fasta_indexes.loc entry would look like this:
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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15 #
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff changeset
16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff changeset
17 #
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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18 #and your /depot/data2/galaxy/hg19/sam/ directory
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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19 #would contain hg19canon.fa and hg19canon.fa.fai files.
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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20 #
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff changeset
21 #Your fasta_indexes.loc file should include an entry per line for
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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22 #each index set you have stored. The file in the path does actually
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff changeset
23 #exist, but it should never be directly used. Instead, the name serves
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff changeset
24 #as a prefix for the index file. For example:
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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25 #
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff changeset
27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff changeset
28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa
5f8d9309058b planemo upload for repository https://github.com/LUMC/lumc-galaxy-tools/tree/master/data_manager_select_index_by_path commit b3f86a0c89c2956f40ee0d462cb31a60eb91724a
rhpvorderman
parents:
diff changeset
29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa