docs: Documentation update (#491)

* [fix] (template): Missing code in wrappers' doc. Error #187

* documentation update

* fix wrong file edition

Co-authored-by: tdayris <[email protected]>

Author: tdayris

bio/adapterremoval/meta.yaml

@@ -1,17 +1,20 @@
 name: "AdapterRemoval"
 description: rapid adapter trimming, identification, and read merging.
+url: https://adapterremoval.readthedocs.io/en/latest/
 authors:
   - Filipe G. Vieira
 input:
-  - raw fastq file with R1 reads
-  - raw fastq file with R2 reads (PE only)
+  - sample:
+    - raw fastq file with R1 reads
+    - raw fastq file with R2 reads (PE only)
 output:
-  - trimmed fastq file with R1 reads
-  - trimmed fastq file with R2 reads (PE only)
-  - fastq file with singleton reads (PE only; PE reads for which the mate has been discarded)
-  - fastq file with collapsed reads (PE only; overlapping mate-pairs which have been merged into a single read)
-  - fastq file with collapsed truncated reads (PE only; collapsed reads that were quality trimmed)
-  - fastq file with discarded reads (reads that did not pass filters)
-  - settings and stats file
+  - fq: path to single fastq file (SE only)
+  - fq1: path to fastq R1 (PE only)
+  - fq2: path to fastq R2 (PE only)
+  - singleton: fastq file with singleton reads (PE only; PE reads for which the mate has been discarded)
+  - collapsed: fastq file with collapsed reads (PE only; overlapping mate-pairs which have been merged into a single read)
+  - collapsed_trunc: fastq file with collapsed truncated reads (PE only; collapsed reads that were quality trimmed)
+  - discarded: fastq file with discarded reads (reads that did not pass filters)
+  - settings: settings and stats file
 notes: |
-  * For more information see, https://adapterremoval.readthedocs.io/en/latest/
+  * All output files, except for 'settings', must be compressed the same way (gz, or bz2).

bio/arriba/meta.yaml

@@ -1,4 +1,18 @@
 name: "arriba"
+url: https://github.com/suhrig/arriba
 description: Detect gene fusions from chimeric STAR output
 authors:
   - Jan Forster
+input:
+  - bam: Path to bam formatted alignment file from STAR
+  - genome: Path to fasta formatted genome sequence
+  - annotation: Path to GTF formatted genome annotation
+output:
+  - fusions: Path to output fusion file
+params:
+  - known_fusions: Path to known fusions file, see `official documentation on known fusions <https://arriba.readthedocs.io/en/latest/input-files/#known-fusions>`_ for more information.
+  - blacklist: Path to blacklist file, see `official documentation on blacklist <https://arriba.readthedocs.io/en/latest/input-files/#blacklist>`_ for more information.
+  - sv_file: Path to structural variations calls from WGS, see `official documentation on SV <https://arriba.readthedocs.io/en/latest/input-files/#structural-variant-calls-from-wgs>`_ for more information.
+  - extra: Other `optional parameters <https://arriba.readthedocs.io/en/latest/command-line-options/>`_
+notes: |
+  This tool/wrapper does not handle multi threading.

bio/art/profiler_illumina/meta.yaml

@@ -1,6 +1,15 @@
 name: art_profiler_illumina
+url: https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm
 description: Use the art profiler to create a base quality score profile for
   Illumina read data from a fastq file.
 authors:
   - David Laehnemann
   - Victoria Sack
+input:
+  - Path to fastq-formatted input file (first place in the input list of files)
+output:
+  - Path to txt formatted profile (first place in the output list of files)
+params:
+  - Extra parameters (no keyword mapped parameter)
+notes: |
+  Your input file must have one of the following extensions: fastq, fastq.gz, fq or fq.gz

bio/assembly-stats/meta.yaml

@@ -1,12 +1,14 @@
 name: "assembly-stats"
 description: Generates report of summary statistics for a genome assembly
+url: https://github.com/sanger-pathogens/assembly-stats
 authors:
   - Pathogen Informatics, Wellcome Sanger Institute (assembly-stats tool) - https://github.com/sanger-pathogens
   - Max Cummins (Snakemake wrapper [unaffiliated with Wellcome Sanger Institute])
 input:
-  - Genomic assembly (fasta format)
+  - assembly: Genomic assembly (fasta format)
 output:
-  - Assembly statistics (format of your choosing, default = tab-delimited)
+  - assembly_stats: Assembly statistics (format of your choosing, default = tab-delimited)
+params:
+  - extra: Optional parameters, see `assembly-stats official documentation <https://github.com/sanger-pathogens/assembly-stats#usage>`_
 notes: |
-  * The `extra` param allows for additional program arguments.
-  * For more inforamtion see https://github.com/sanger-pathogens/assembly-stats
+  This tool/wrapper does not handle multi threading

bio/bamtools/filter/meta.yaml

@@ -1,8 +1,20 @@
 name: bamtools filter
-description: Filters BAM files. For more information about bamtools see `bamtools documentation <http://stab.st-andrews.ac.uk/wiki/index.php/Bamtools>`_ and `bamtools source code <https://github.com/pezmaster31/bamtools>`_.
+url: https://github.com/pezmaster31/bamtools
+description: Filters BAM files. For more information about bamtools see `bamtools documentation <http://stab.st-andrews.ac.uk/wiki/index.php/Bamtools>`_
 authors:
   - Antonie Vietor
 input:
-  - bam files (.bam)
+  - bam files (.bam), must be in first position
 output:
-  - bam file (.bam)
+  - bam file (.bam), must be in first position
+params:
+  - tags: filtering tags
+  - min_size: minimum insert size
+  - max_size: maximum insert size
+  - min_length: minimum read length
+  - max_length: maximum read length
+  - additional_params: Other filtering and optional parameters
+notes: |
+  A complete usage documentation is available here: https://raw.githubusercontent.com/wiki/pezmaster31/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf
+
+  This tool/wrapper does not handle multi threading

bio/bamtools/filter_json/meta.yaml

@@ -1,9 +1,16 @@
 name: bamtools filter with json
-description: Filters BAM files with JSON-script for filtering parameters and rules. For more information about bamtools see `bamtools documentation <http://stab.st-andrews.ac.uk/wiki/index.php/Bamtools>`_ and `bamtools source code <https://github.com/pezmaster31/bamtools>`_.
+url: https://github.com/pezmaster31/bamtools
+description: Filters BAM files with JSON-script for filtering parameters and rules. For more information about bamtools see `bamtools documentation <http://stab.st-andrews.ac.uk/wiki/index.php/Bamtools>`_
 authors:
   - Antonie Vietor
 input:
-  - bam files (.bam)
-  - json file (.json)
+  - bam files (.bam), must be in first position
 output:
-  - bam file (.bam)
+  - bam file (.bam), must be in first position
+params:
+  - json: Path to filter file, json formatted.
+  - region: see documentation for more information about multiple formats.
+notes: |
+  A complete usage documentation is available here: https://raw.githubusercontent.com/wiki/pezmaster31/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf
+
+  This tool/wrapper does not handle multi threading

bio/bamtools/split/meta.yaml

@@ -1,8 +1,15 @@
 name: bamtools split
+url: https://github.com/pezmaster31/bamtools
 description: Split bam file into sub files, default by reference
 authors:
   - Patrik Smeds
 input:
-  - bam file
+  - bam file, this must be the only file in input.
 output:
-  - multiple bam file
+  - multiple bam file multiple formats.
+params:
+  - extra: Optional parameters
+notes: |
+  A complete usage documentation is available here: https://raw.githubusercontent.com/wiki/pezmaster31/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf
+
+  This tool/wrapper does not handle multi threading

bio/bamtools/stats/meta.yaml

@@ -1,8 +1,14 @@
 name: bamtools stats
+url: https://github.com/pezmaster31/bamtools
 description: Use bamtools to collect statistics from a BAM file. For more information about bamtools see `bamtools documentation <http://stab.st-andrews.ac.uk/wiki/index.php/Bamtools>`_ and `bamtools source code <https://github.com/pezmaster31/bamtools>`_.
 authors:
   - Antonie Vietor
 input:
-  - bam files (.bam)
+  - bam files (.bam), must be in first position
 output:
-  - bamstats file (.bamstats)
+  - bamstats file (.bamstats), must be in first position
+params:
+  - Optional parameters as first and only value.
+notes: |
+  A complete usage documentation is available here: https://raw.githubusercontent.com/wiki/pezmaster31/bamtools/Tutorial_Toolkit_BamTools-1.0.pdf
+  This tool/wrapper does not handle multi threading

bio/bbtools/bbduk/meta.yaml

@@ -1,18 +1,19 @@
 name: BBDuk
+url: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/
 description: |
   Run BBDuk.
 authors:
   - Filipe G. Vieira
 input:
-  - raw fastq file with R1 reads
-  - raw fastq file with R2 reads (optional)
+  - sample: list of paths. Raw fastq file with R1 reads, raw fastq file with R2 reads (PE only, optional)
 output:
-  - trimmed fastq file with R1 reads
-  - trimmed fastq file with R2 reads (optional)
-  - fastq file with singleton reads (optional)
-  - fastq file with discarded reads (optional) 
-  - stats file (optonal)
+  - trimmed: trimmed fastq file with R1 reads, trimmed fastq file with R2 reads (PE only, optional)
+  - singleton: fastq file with singleton reads (optional)
+  - discarded: fastq file with discarded reads (optional)
+  - stats: stats file (optonal)
+params:
+  - extra: Optional parameters
+  - adapters: Literal adapters sequences
 notes: |
   * The `java_opts` param allows for additional arguments to be passed to the java compiler, e.g. "-XX:ParallelGCThreads=10" (not for `-XmX` or `-Djava.io.tmpdir`, since they are handled automatically).
   * The `extra` param allows for additional program arguments.
-  * For more information see, https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/