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This commit is contained in:
Aurelie Bonin
2014-01-31 14:51:50 +00:00
parent 927157c735
commit b4c71741c5
2 changed files with 12 additions and 12 deletions
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18
doc/sphinx/source/optionsSet/inputformat.txt
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@ -8,11 +8,11 @@ Sequence annotated format
.. cmdoption:: --genbank .. cmdoption:: --genbank
Input file is in :doc:`genbank <../genbank>` format Input file is in :doc:`genbank <../genbank>` format.
.. cmdoption:: --embl .. cmdoption:: --embl
Input file is in :doc:`embl <../embl>` format Input file is in :doc:`embl <../embl>` format.
:doc:`fasta <../fasta>` related format :doc:`fasta <../fasta>` related format
....................................... .......................................
@ -21,7 +21,7 @@ Sequence annotated format
.. cmdoption:: --fasta .. cmdoption:: --fasta
Input file is in :doc:`fasta <../fasta>` format (including Input file is in :doc:`fasta <../fasta>` format (including
OBITools :doc:`fasta <../fasta>` extentions) OBITools :doc:`fasta <../fasta>` extensions).
:doc:`fastq <../fastq>` related format :doc:`fastq <../fastq>` related format
....................................... .......................................
@ -29,33 +29,33 @@ Sequence annotated format
.. cmdoption:: --sanger .. cmdoption:: --sanger
Input file is in Sanger :doc:`fastq <../fastq>` format (standard Input file is in Sanger :doc:`fastq <../fastq>` format (standard
:doc:`fastq <../fastq>` used by HiSeq/MiSeq sequencers) :doc:`fastq <../fastq>` used by HiSeq/MiSeq sequencers).
.. cmdoption:: --solexa .. cmdoption:: --solexa
Input file is in :doc:`fastq <../fastq>` format produced by Input file is in :doc:`fastq <../fastq>` format produced by
Solexa (Ga IIx) sequencers Solexa (Ga IIx) sequencers.
ecoPCR related format ecoPCR related format
..................... .....................
.. cmdoption:: --ecopcr .. cmdoption:: --ecopcr
Input file is in :doc:`ecoPCR <../formats>` format Input file is in :doc:`ecoPCR <../formats>` format.
.. cmdoption:: --ecopcrdb .. cmdoption:: --ecopcrdb
Input is an :doc:`ecoPCR <../formats>` database Input is an :doc:`ecoPCR <../formats>` database.
Specifying the sequence type Specifying the sequence type
............................ ............................
.. cmdoption:: --nuc .. cmdoption:: --nuc
Input file contains nucleic sequences Input file contains nucleic sequences.
.. cmdoption:: --prot .. cmdoption:: --prot
Input file contains protein sequences Input file contains protein sequences.

6
doc/sphinx/source/scripts/obitab.rst
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@ -6,7 +6,7 @@
.. cmdoption:: -n <NOT AVAILABLE STRING>, --na-string=<NOT AVAILABLE STRING> .. cmdoption:: -n <NOT AVAILABLE STRING>, --na-string=<NOT AVAILABLE STRING>
String writed in the table for the not available values String written in the table for the not available values
(default value ``NA``). (default value ``NA``).
.. cmdoption:: --output-field-separator=<STRING> .. cmdoption:: --output-field-separator=<STRING>
@ -26,8 +26,8 @@
.. cmdoption:: -a <KEY>, --omit-attribute=<KEY> .. cmdoption:: -a <KEY>, --omit-attribute=<KEY>
Adds attribute to the omit list. Attributes whose key is Attributes whose key is in this list will not be printed in
in this list will not be printed in the output tab file. the output tab file.
.. include:: ../optionsSet/inputformat.txt .. include:: ../optionsSet/inputformat.txt