Mercurial > repos > yating-l > hubarchivecreatortest
annotate bigPsl.as @ 3:fa990284327b draft default tip
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit ac73da32d59853ca563e7939d05016a6f3a6899e-dirty
| author | yating-l |
|---|---|
| date | Mon, 30 Oct 2017 11:58:31 -0400 |
| parents | 85195e0d4b71 |
| children |
| rev | line source |
|---|---|
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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1 table bigPsl |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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2 "bigPsl pairwise alignment" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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3 ( |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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4 string chrom; "Reference sequence chromosome or scaffold" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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5 uint chromStart; "Start position in chromosome" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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6 uint chromEnd; "End position in chromosome" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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7 string name; "Name or ID of item, ideally both human readable and unique" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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8 uint score; "Score (0-1000)" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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9 char[1] strand; "+ or - for strand" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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10 uint thickStart; "Start of where display should be thick (start codon)" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
11 uint thickEnd; "End of where display should be thick (stop codon)" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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12 uint reserved; "RGB value (use R,G,B string in input file)" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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13 int blockCount; "Number of blocks" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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14 int[blockCount] blockSizes; "Comma separated list of block sizes" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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15 int[blockCount] chromStarts; "Start positions relative to chromStart" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
16 |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
17 uint oChromStart;"Start position in other chromosome" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
18 uint oChromEnd; "End position in other chromosome" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
19 char[1] oStrand; "+ or - for other strand" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
20 uint oChromSize; "Size of other chromosome." |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
21 int[blockCount] oChromStarts; "Start positions relative to oChromStart" |
|
85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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22 |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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23 lstring oSequence; "Sequence on other chrom (or edit list, or empty)" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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24 string oCDS; "CDS in NCBI format" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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25 |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
26 uint chromSize;"Size of target chromosome" |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
27 |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
28 uint match; "Number of bases matched." |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
29 uint misMatch; " Number of bases that don't match " |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
30 uint repMatch; " Number of bases that match but are part of repeats " |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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31 uint nCount; " Number of 'N' bases " |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
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32 ) |
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85195e0d4b71
planemo upload for repository https://github.com/goeckslab/hub-archive-creator commit b1ae7349f118a0fe7923d765020dfc684cf84116-dirty
yating-l
parents:
diff
changeset
|
33 |