Mercurial > repos > iuc > samtools_cram_to_bam
annotate tool-data/fasta_indexes.loc.sample @ 5:634df184b2a8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit c5ded4208dd70e88596ddc725795a2401773f02d"
| author | iuc |
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| date | Sat, 27 Nov 2021 12:31:35 +0000 |
| parents | 0637018367e0 |
| children |
| rev | line source |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
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changeset
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1 #This is a sample file distributed with Galaxy that enables tools |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
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changeset
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2 #to use a directory of Samtools indexed sequences data files. You will need |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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3 #to create these data files and then create a fasta_indexes.loc file |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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4 #similar to this one (store it in this directory) that points to |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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5 #the directories in which those files are stored. The fasta_indexes.loc |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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6 #file has this format (white space characters are TAB characters): |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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7 # |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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8 # <unique_build_id> <dbkey> <display_name> <file_base_path> |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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9 # |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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10 #So, for example, if you had hg19 Canonical indexed stored in |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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11 # |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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12 # /depot/data2/galaxy/hg19/sam/, |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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13 # |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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14 #then the fasta_indexes.loc entry would look like this: |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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15 # |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
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changeset
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16 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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17 # |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
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18 #and your /depot/data2/galaxy/hg19/sam/ directory |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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19 #would contain hg19canon.fa and hg19canon.fa.fai files. |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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20 # |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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21 #Your fasta_indexes.loc file should include an entry per line for |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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22 #each index set you have stored. The file in the path does actually |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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23 #exist, but it should never be directly used. Instead, the name serves |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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24 #as a prefix for the index file. For example: |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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25 # |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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26 #hg18canon hg18 Human (Homo sapiens): hg18 Canonical /depot/data2/galaxy/hg18/sam/hg18canon.fa |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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27 #hg18full hg18 Human (Homo sapiens): hg18 Full /depot/data2/galaxy/hg18/sam/hg18full.fa |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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28 #hg19canon hg19 Human (Homo sapiens): hg19 Canonical /depot/data2/galaxy/hg19/sam/hg19canon.fa |
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0637018367e0
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/cram_to_bam commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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29 #hg19full hg19 Human (Homo sapiens): hg19 Full /depot/data2/galaxy/hg19/sam/hg19full.fa |