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annotate tool-data/lastz_seqs.loc.sample @ 0:16209195224c draft default tip

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
author rnateam
date Fri, 25 Nov 2016 09:38:28 -0500
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16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
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1 #This is a sample file distributed with Galaxy that enables tools
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
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diff changeset
2 #to use a directory of 2bit genome files for use with Lastz. You will
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
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3 #need to supply these files and then create a lastz_seqs.loc file
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
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diff changeset
4 #similar to this one (store it in this directory) that points to
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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5 #the directories in which those files are stored. The lastz_seqs.loc
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
diff changeset
6 #file has this format (white space characters are TAB characters):
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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7 #
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
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8 #<unique_build_id> <display_name> <file_path>
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
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9 #
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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10 #So, for example, if your lastz_seqs.loc began like this:
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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11 #
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
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12 #hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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13 #hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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14 #mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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15 #
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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16 #then your /depot/data2/galaxy/twobit/ directory
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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17 #would need to contain the following 2bit files:
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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18 #
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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19 #-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.2bit
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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20 #-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg19.2bit
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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21 #-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 mm9.2bit
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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22 #
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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23 #Your lastz_seqs.loc file should include an entry per line for
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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24 #each file you have stored that you want to be available. Note that
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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25 #your files should all have the extension '2bit'.
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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26 #
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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27 #Note that for backwards compatibility with workflows, the unique ID of
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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28 #an entry must be the path that was in the original loc file, because that
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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29 #is the value stored in the workflow for that parameter.
16209195224c planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/pipmir commit 5937e8d61ae1203ebf2a536c669ba701b485cd1a
rnateam
parents:
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30 #