Reorganization of the documentation book directory

Former-commit-id: 095acaf9c8649b0e527c6253dc79330feedac865

doc/lib/options/_input.qmd

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+{{< include ../lib/options/input/_embl.qmd >}}
+
+{{< include ../lib/options/input/_genbank.qmd >}}
+
+{{< include ../lib/options/input/_ecopcr.qmd >}}
+
+
+**\--input-OBI-header**
+
+: OBITools V4 introduced a new format based on [JSON](https://en.wikipedia.org/wiki/JSON) for storing annotations in the FASTA and FASTQ title lines. Nevertheless they continue to parse the old OBITools format for these annotation (`KEY=VALUE;`). Both formats for annotations are automatically recognizd. That option force the parsing of the annotations following the genuine OBITools format.
+
+**\--input-json-header**
+
+: Forces the parsing of the FASTA and FASTQ annotations usng the new OBITools JSON based format. 
+
+**\--solexa**
+
+: Sequence quality scores in FASTQ format are supposed to follow to Sanger convention for their ASCII encoding. Somme old raw data files produced by Solexa sequencers used another encoding schema. That options allows to correctly read these ald FASTQ files.  
+
+**\--no-order**
+
+: OBITools V4 are massively parallelized. When several input files are provided this option allows to processed them in parallel. But the order of the file indicated on the command line will no more be related to the order of the sequences in the output of the command.

doc/lib/options/_output.qmd

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+**\--fasta-output** 
+
+**\--fastq-output** 
+
+**\--output-OBI-header**, **-O** 
+
+**\--output-json-header**
+
+{{< include ../lib/options/output/_out.qmd >}}
+
+{{< include ../lib/options/output/_compress.qmd >}}

doc/lib/options/_system.qmd

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+**Helpful options**
+
+{{< include ../lib/options/system/_help.qmd >}}
+
+{{< include ../lib/options/system/_no-progressbar.qmd >}}
+
+**Managing parallel execution**
+
+{{< include ../lib/options/system/_max-cpu.qmd >}}
+
+{{< include ../lib/options/system/_workers.qmd >}}
+
+**OBITools debuging related options**
+
+{{< include ../lib/options/system/_debug.qmd >}}

doc/lib/options/input/_ecopcr.qmd

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+**\--ecopcr**
+
+: indicates that the input data follow the ecopcr tabular format produced by [ecoPCR](https://metabarcoding.org/ecopcr).

doc/lib/options/input/_embl.qmd

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+**\--embl**
+
+: indicates that the input data follow the EMBL flatfile format.
+

doc/lib/options/input/_genbank.qmd

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+**\--genbank**
+
+: indicates that the input data follow the Genbank flatfile format.
+

doc/lib/options/output/_compress.qmd

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+**\--compress**, **-Z**
+
+: The ouput is compressed following the [gzip](https://en.wikipedia.org/wiki/Gzip) format.

doc/lib/options/output/_out.qmd

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+**\--out** _FILENAME_, **-o**
+
+: OBITools, as all standard UNIX tools, print their results to the standard output (`stdout`). To save them, stdout must be redirected to a file. That option allows to specify explicitely an output file to the command. This is especially useful when OBITools are processing paired files. In that later case, the indicated output file names is modified by adding to it the *\_R1* (forward file) and *\_R2* (reverse file) suffix just before the extensions (*e.g.* sequence.fasta becomes sequence_R1.fasta and sequence_R2.fasta). If that option is not specified and paired files are processed only the forward data are ouputed to the _stdout_.

doc/lib/options/selection/_max-count.qmd

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+**\--max-count** | **-C** _COUNT_
+
+: only sequences reprensenting no more than _COUNT_ reads will be selected. That option rely on the `count` attribute. If the `count` attribute is not defined for a sequence record, it is assumed equal to $1$. 

doc/lib/options/selection/_min-count.qmd

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+**\--min-count** | **-c** _COUNT_
+
+: only sequences reprensenting at least _COUNT_ reads will be selected. That option rely on the `count` attribute. If the `count` attribute is not defined for a sequence record, it is assumed equal to $1$. 

doc/lib/options/system/_debug.qmd

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+**\--debug**
+

doc/lib/options/system/_help.qmd

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+**\--help**, **-h**
+
+: Display a friendly help message.

doc/lib/options/system/_max-cpu.qmd

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+**\--max-cpu**
+
+: OBITools V4 are able to run in parallel on all the CPU cores available on the computer. It is sometime required to limit the computation to a smaller number of cores. That option specify the maximum number of cores that the OBITools command can use. This behaviour can also be set up using the `OBIMAXCPU` environment variable.

doc/lib/options/system/_no-progressbar.qmd

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+**\--no-progressbar**
+

doc/lib/options/system/_workers.qmd

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+**\--workers**, **-w**
+