Mercurial > repos > galaxyp > psm_to_sam

annotate tool-data/customProDB.loc.sample @ 0:90ecb65017a0 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
author galaxyp
date Wed, 17 May 2017 20:23:27 -0400
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90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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1 #This file lists the locations and dbkeys of all the fasta files
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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2 #under the "genome" directory (a directory that contains a directory
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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3 #for each build). The script extract_fasta.py will generate the file
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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4 #all_fasta.loc. This file has the format (white space characters are
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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5 #TAB characters):
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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6 #
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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7 #<unique_build_id> <dbkey> <display_name> <file_path>
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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8 #
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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9 #So, all_fasta.loc could look something like this:
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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10 #
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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11 #apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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12 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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13 #hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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14 #mm10 mm10 Mouse (Mus musculus): mm10 /path/to/genome/mm10/mm10.fa
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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15 #
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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16 #Your all_fasta.loc file should contain an entry for each individual
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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17 #fasta file. So there will be multiple fasta files for each build,
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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18 #such as with hg19 above.
90ecb65017a0 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/psm2sam commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
galaxyp
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19 #