feat: Xsv (complete subcomand suite) (#1430)

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### Description

This PR adds [xsv](https://github.com/BurntSushi/xsv) select, to the
list of available wrappers.

### QC
<!-- Make sure that you can tick the boxes below. -->

* [X] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).

---------

Co-authored-by: tdayris <tdayris@gustaveroussy.fr>
Co-authored-by: tdayris <thibault.dayris@gustaveroussy.fr>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: snakedeploy-bot[bot] <115615832+snakedeploy-bot[bot]@users.noreply.github.com>
Co-authored-by: Felix Mölder <felix.moelder@uni-due.de>
Co-authored-by: Christopher Schröder <christopher.schroeder@tu-dortmund.de>

bio/xsv/environment.yaml

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+channels:
+  - conda-forge
+  - nodefaults
+dependencies:
+  - xsv=0.13.0

bio/xsv/meta.yaml

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+name: xsv
+url: https://github.com/BurntSushi/xsv
+description: >
+  Perform various operations over CSV/TSV tables.
+authors:
+  - Thibault Dayris
+input:
+  - table: Path to CSV/TSV table.
+output:
+  - Path the result file / directory
+params:
+  - extra: Optional arguments for `xsv`. For TSV files, `--delimiter` is automatically set to a tabulation.
+  - subcommand: xsv subcommand among `cat`, `count`, `fixlengths`, `flatten`, `fmt`, `frequency`, `headers`, `index`, `input`, `join`, `sample`, `search`, `select`, `slice`, `sort`, `split`, `stats`, or `table`
+notes: |
+  Adding table(s) index(es) to the input file list makes many subcommands faster.

bio/xsv/test/Snakefile

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+### Concatenation subcommand ###
+rule test_xsv_cat_rows:
+    input:
+        table=["table.csv", "right.csv"],
+    output:
+        "xsv_catrows.csv",
+    threads: 1
+    log:
+        "xsv/catrow.log",
+    params:
+        subcommand="cat rows",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+rule test_xsv_cat_cols:
+    input:
+        table=["table.csv", "right.csv"],
+    output:
+        "xsv_catcols.csv",
+    threads: 1
+    log:
+        "xsv/catcol.log",
+    params:
+        subcommand="cat columns",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Count subcommand ###
+rule test_xsv_count:
+    input:
+        table="table.csv",
+    output:
+        "xsv_count.csv",
+    threads: 1
+    log:
+        "xsv/count.log",
+    params:
+        subcommand="count",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+rule test_xsv_count_tsv_input:
+    input:
+        table="table.tsv",
+    output:
+        "xsv_count.tsv_as_input.csv",
+    threads: 1
+    log:
+        "xsv/count.log",
+    params:
+        subcommand="count",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Fix lengths subcommand ###
+rule test_xsv_fixlength:
+    input:
+        table="table.csv",
+    output:
+        "xsv_fixlength.csv",
+    threads: 1
+    log:
+        "xsv/fixlength.log",
+    params:
+        subcommand="fixlengths",
+        extra="--length 20",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Flatten subcommand ###
+rule test_xsv_flatten:
+    input:
+        table="table.csv",
+    output:
+        "xsv_flatten.csv",
+    threads: 1
+    log:
+        "xsv/flatten.log",
+    params:
+        subcommand="flatten",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Format subcommand ###
+rule test_xsv_fmt:
+    input:
+        table="table.csv",
+    output:
+        "xsv_fmt.tsv",
+    threads: 1
+    log:
+        "xsv/fmt.log",
+    params:
+        subcommand="fmt",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Frequency subcommand ###
+rule test_xsv_frequency:
+    input:
+        table="table.csv",
+    output:
+        "xsv_frequency.csv",
+    threads: 1
+    log:
+        "xsv/frequency.log",
+    params:
+        subcommand="frequency",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Headers subcommand ###
+rule test_xsv_headers:
+    input:
+        table="table.csv",
+    output:
+        "xsv_headers.csv",
+    threads: 1
+    log:
+        "xsv/headers.log",
+    params:
+        subcommand="headers",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+rule test_xsv_headers_list:
+    input:
+        table=["table.csv", "right.csv"],
+    output:
+        "xsv_headers_all.csv",
+    threads: 1
+    log:
+        "xsv/headers_all.log",
+    params:
+        subcommand="headers",
+        extra="--intersect",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Index subcommand ###
+rule test_xsv_index:
+    input:
+        table="table.csv",
+    output:
+        "table.csv.idx",
+    threads: 1
+    log:
+        "xsv/index.log",
+    params:
+        subcommand="index",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Input subcommand ###
+rule test_xsv_input:
+    input:
+        table="table.csv",
+    output:
+        "xsv_input.csv",
+    threads: 1
+    log:
+        "xsv/input.log",
+    params:
+        subcommand="input",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Join subcommand ###
+rule test_xsv_join:
+    input:
+        table=["table.csv", "right.csv"],
+    output:
+        "xsv_join.csv",
+    threads: 1
+    log:
+        "xsv/join.log",
+    params:
+        subcommand="join",
+        col1="gene_id",
+        col2="gene_id",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Sample subcommand ###
+rule test_xsv_sample:
+    input:
+        table="table.csv",
+    output:
+        "xsv_sample.csv",
+    threads: 1
+    log:
+        "xsv/sample.log",
+    params:
+        subcommand="sample",
+        extra="1",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Search subcommand ###
+rule test_xsv_search:
+    input:
+        table="table.csv",
+    output:
+        "xsv_search.csv",
+    threads: 1
+    log:
+        "xsv/search.log",
+    params:
+        subcommand="search",
+        extra="--select gene_id ENSG[0-9]+",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Select subcommand ###
+rule test_xsv_select:
+    input:
+        table="table.csv",
+    output:
+        "xsv_select.csv",
+    threads: 1
+    log:
+        "xsv/select.log",
+    params:
+        subcommand="select",
+        extra="3-",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Slice subcommand ###
+rule test_xsv_slice:
+    input:
+        table="table.csv",
+    output:
+        "xsv_slice.csv",
+    threads: 1
+    log:
+        "xsv/slice.log",
+    params:
+        subcommand="slice",
+        extra="-i 2",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Sort subcommand ###
+rule test_xsv_sort:
+    input:
+        table="table.csv",
+    output:
+        "xsv_sort.csv",
+    threads: 1
+    log:
+        "xsv/sort.log",
+    params:
+        subcommand="sort",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Split subcommand ###
+rule test_xsv_split:
+    input:
+        table="table.csv",
+    output:
+        directory("xsv_split"),
+    threads: 1
+    log:
+        "xsv/split.log",
+    params:
+        subcommand="split",
+        extra="-s 2",
+    wrapper:
+        "master/bio/xsv"
+
+
+rule test_xsv_split_list:
+    input:
+        table="table.csv",
+    output:
+        expand("xsv_split/{nb}.csv", nb=["0", "1"]),
+    threads: 1
+    log:
+        "xsv/split.log",
+    params:
+        subcommand="split",
+        extra="-s 1",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Stat subcommand ###
+rule test_xsv_stats:
+    input:
+        table="table.csv",
+    output:
+        "xsv_stats.txt",
+    threads: 1
+    log:
+        "xsv/stats.log",
+    params:
+        subcommand="stats",
+        extra="",
+    wrapper:
+        "master/bio/xsv"
+
+
+### Table subcommand ###
+rule test_xsv_table:
+    input:
+        table="right.csv",
+    output:
+        "xsv_table.txt",
+    threads: 1
+    log:
+        "xsv/table.log",
+    params:
+        subcommand="table",
+        extra="",
+    wrapper:
+        "master/bio/xsv"

bio/xsv/test/right.csv

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+gene_id,s4,s5,s6
+ENSG03,24.5,15,85
+ENSG02,12,157,0.2

bio/xsv/test/table.csv

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+gene_id,s1,s2,s3
+ENSG01,14.5,15,75
+ENSG02,12,57,0.2

bio/xsv/test/table.tsv

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+gene_id	s1	s2	s3
+ENSG01	14.5	15	75
+ENSG02	12	57	0.2