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ENH: update action and parameter descriptions
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@nbokulich
nbokulich committed Jan 31, 2024
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Showing 1 changed file with 70 additions and 70 deletions.
140 changes: 70 additions & 70 deletions q2_moshpit/plugin_setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -175,8 +175,8 @@
('hits', T_kraken_out_hits),
],
input_descriptions={
"seqs": "Sequences to be classified. Both, single-/paired-end reads"
"and assembled MAGs, can be provided.",
"seqs": "Sequences to be classified. Single-/paired-end reads,"
"contigs, or assembled MAGs can be provided.",
"kraken2_db": "Kraken 2 database.",
},
parameter_descriptions={
Expand All @@ -188,8 +188,8 @@
'hits': 'Output files produced by Kraken2.',
},
name='Perform taxonomic classification of reads or MAGs using Kraken 2.',
description='This method uses Kraken 2 to classify provided NGS reads '
'or MAGs into taxonomic groups.',
description='Use Kraken 2 to classify provided DNA sequence reads, '
'contigs, or MAGs into taxonomic groups.',
citations=[citations["wood2019"]]
)

Expand All @@ -205,8 +205,8 @@
('hits', T_kraken_out_hits),
],
input_descriptions={
"seqs": "The sequences to be classified. Single-end or paired-end "
"reads, contigs, or MAGs can be provided.",
"seqs": "Sequences to be classified. Single-/paired-end reads,"
"contigs, or assembled MAGs can be provided.",
"kraken2_db": "Kraken 2 database.",
},
parameter_descriptions=kraken2_param_descriptions,
Expand All @@ -215,8 +215,8 @@
'hits': 'Output files produced by Kraken2.',
},
name='Perform taxonomic classification of reads or MAGs using Kraken 2.',
description='This method uses Kraken 2 to classify provided NGS reads '
'or MAGs into taxonomic groups.',
description='Use Kraken 2 to classify provided DNA sequence reads, '
'contigs, or MAGs into taxonomic groups.',
citations=[citations["wood2019"]]
)

Expand Down Expand Up @@ -258,8 +258,8 @@
inputs={"kraken2_outputs": List[T_kraken_collate_outputs_in]},
parameters={},
outputs={"collated_kraken2_outputs": T_kraken_collate_outputs_out},
name="Collate kraken2 outputs",
description="Collates kraken2 outputs"
name="Collate kraken2 outputs.",
description="Collates kraken2 outputs."
)

plugin.methods.register_function(
Expand All @@ -285,10 +285,13 @@
parameter_descriptions={
'threshold': 'Bracken: number of reads required PRIOR to abundance '
'estimation to perform re-estimation.',
'read_len': ('Bracken: read length to get all classifications for. '
'For paired end data (e.g., 2x150) this should be set '
'to the length of the single-end reads (e.g., 150).'),
'level': 'Bracken: taxonomic level to estimate abundance at.'
'read_len': 'Bracken: the ideal length of reads in your sample. '
'For paired end data (e.g., 2x150) this should be set '
'to the length of the single-end reads (e.g., 150).',
'level': 'Bracken: specifies the taxonomic rank to analyze. Each '
'classification at this specified rank will receive an '
'estimated number of reads belonging to that rank after '
'abundance estimation.'
},
output_descriptions={
'reports': 'Reports modified by Bracken.',
Expand Down Expand Up @@ -340,7 +343,7 @@
'ignored in comparisons.',
'no_masking': 'Avoid masking low-complexity sequences prior to '
'building; masking requires dustmasker or segmasker '
'to be installed in PATH',
'to be installed in PATH.',
'max_db_size': 'Maximum number of bytes for Kraken 2 hash table; '
'if the estimator determines more would normally be '
'needed, the reference library will be downsampled '
Expand All @@ -358,9 +361,10 @@
'bracken_database': 'Bracken database.'
},
name='Build Kraken 2 database.',
description='This method builds a Kraken 2/Bracken databases from '
'provided DNA sequences or simply fetches pre-built '
'versions from an online resource.',
description='This method builds Kraken 2 and Bracken databases either (1) '
'from provided DNA sequences to build a custom database, or '
'(2) simply fetches pre-built versions from an online '
'resource.',
citations=[citations["wood2019"], citations["lu2017"]]
)

Expand All @@ -380,10 +384,10 @@
},
name="Inspect a Kraken 2 database.",
description="This method generates a report of identical format to those "
"generated by classify_kraken2, with the interpretation being "
"instead of reporting the number of inputs classified to a "
"taxon/clade, the number of minimizers mapped to a "
"taxon/clade are reported.",
"generated by classify_kraken2, with a slightly different "
"interpretation. Instead of reporting the number of inputs "
"classified to a taxon/clade, the report displays the number "
"of minimizers mapped to each taxon/clade.",
citations=[citations["wood2019"]],
)

Expand Down Expand Up @@ -420,6 +424,16 @@
citations=[]
)

select_features_taxonomy_description = (
'Output taxonomy. Infra-clade ranks are ignored unless if they are '
'strain-level. Missing internal ranks are annotated by their next '
'most specific rank, with the exception of k__Bacteria and k__Archaea, '
'which match their domain name.')

select_features_description = (
'Convert a Kraken 2 report, which is an annotated NCBI taxonomy tree, '
'into generic artifacts for downstream analyses.')

plugin.methods.register_function(
function=q2_moshpit.kraken2.kraken2_to_features,
inputs={
Expand All @@ -436,23 +450,17 @@
'reports': 'Per-sample Kraken 2 reports.'
},
parameter_descriptions={
'coverage_threshold': 'The minimum percent coverage required to'
' produce a feature.'
'coverage_threshold': 'The minimum percent coverage required to '
'produce a feature.'
},
output_descriptions={
'table': 'A presence/absence table of selected features. The features'
' are not of even ranks, but will be the most specific rank'
' available.',
'taxonomy': 'Infra-clade ranks are ignored '
'unless they are strain-level. Missing internal ranks '
'are annotated by their next most specific rank, '
'with the exception of k__Bacteria and k__Archaea which '
'match their domain\'s name.',
},
name='Select downstream features from Kraken 2',
description='Convert a Kraken 2 report, which is an annotated NCBI '
'taxonomy tree into generic artifacts for downstream '
'analyses.'
'table': 'A presence/absence table of selected features. The features '
'are not of even ranks, but will be the most specific rank '
'available.',
'taxonomy': select_features_taxonomy_description,
},
name='Select features from a Kraken 2 report.',
description=select_features_description
)

plugin.methods.register_function(
Expand All @@ -477,16 +485,10 @@
# 'taxonomic assignments of its contigs. '
},
output_descriptions={
'taxonomy': 'Infra-clade ranks are ignored '
'unless they are strain-level. Missing internal ranks '
'are annotated by their next most specific rank, '
'with the exception of k__Bacteria and k__Archaea which '
'match their domain\'s name.',
},
name='Select downstream MAG features from Kraken 2',
description='Convert a Kraken 2 report, which is an annotated NCBI '
'taxonomy tree into generic artifacts for downstream '
'analyses.'
'taxonomy': select_features_taxonomy_description,
},
name='Select MAG features from a Kraken 2 report.',
description=select_features_description
)

plugin.methods.register_function(
Expand Down Expand Up @@ -533,15 +535,14 @@
parameters={},
outputs=[("eggnog_db", ReferenceDB[Eggnog])],
output_descriptions={
"eggnog_db": "Artifact containing the eggNOG annotation "
"database."
"eggnog_db": "eggNOG annotation database."
},
name="Fetch the databases necessary to run the "
"eggnog-annotate action.",
description="Downloads eggnog reference database "
"using the `download_eggnog_data.py` script from eggNOG. "
"Here, this script downloads 3 files "
"and creates and artifact with them. At least 80 Gb of "
"and creates an artifact with them. At least 80 Gb of "
"storage space is required to run this action. "
"Links to files: "
"eggnog.db: "
Expand Down Expand Up @@ -589,7 +590,7 @@
},
name="Fetch the databases necessary to run the "
"build-eggnog-diamond-db action.",
description="Downloads eggnog proteome database "
description="Downloads eggnog proteome database. "
"This script downloads 2 files "
"(e5.proteomes.faa and e5.taxid_info.tsv) "
"and creates and artifact with them. At least 18 GB of "
Expand All @@ -606,10 +607,10 @@
output_descriptions={
"taxonomy": "NCBI reference taxonomy."
},
name="Fetch NCBI reference taxonomy",
name="Fetch NCBI reference taxonomy.",
description="Downloads NCBI reference taxonomy from the NCBI FTP server. "
"The resulting artifact is required by the "
"build-custom-diamond-db action if one wished to "
"build-custom-diamond-db action if one wishes to "
"create a Diamond data base with taxonomy features. "
"At least 30 GB of "
"storage space is required to run this action.",
Expand All @@ -631,14 +632,14 @@
'taxon': Int % Range(2, 1579337)
},
parameter_descriptions={
'taxon': "Taxon ID number."
'taxon': "NCBI Taxon ID number."
},
outputs=[("diamond_db", ReferenceDB[Diamond])],
output_descriptions={
"diamond_db": "Complete Diamond reference database for the"
"diamond_db": "Complete Diamond reference database for the "
"specified taxon."
},
name="Create a DIAMOND formatted reference database for the"
name="Create a DIAMOND formatted reference database for the "
"specified taxon.",
description="Creates a DIAMOND database which contains the protein "
"sequences that belong to the specified taxon.",
Expand All @@ -659,14 +660,13 @@
'db_in_memory': Bool,
},
input_descriptions={
'sequences': 'Sequence data of the contigs we want to '
'search for hits using the Diamond Database',
'diamond_db': 'The filepath to an artifact containing the '
'Diamond database',
'sequences': 'Contigs or MAGs to '
'search against the Diamond Database.',
'diamond_db': 'The Diamond database.',
},
parameter_descriptions={
'num_cpus': 'Number of CPUs to utilize. \'0\' will '
'use all available.',
'use all available CPUs.',
'db_in_memory': 'Read database into memory. The '
'database can be very large, so this '
'option should only be used on clusters or other '
Expand All @@ -676,10 +676,9 @@
('eggnog_hits', SampleData[BLAST6]),
('table', FeatureTable[Frequency])
],
name='Run eggNOG search using diamond aligner',
description="This method performs the steps by which we find our "
"possible target sequences to annotate using the diamond "
"search functionality from the eggnog `emapper.py` script",
name='Run eggNOG search using diamond aligner.',
description="Use Diamond and eggNOG to align contig or MAG sequences "
"against the Diamond database.",
citations=[
citations["buchfink_sensitive_2021"],
citations["huerta_cepas_eggnog_2019"]
Expand All @@ -702,7 +701,7 @@
'machines with enough memory.',
},
outputs=[('ortholog_annotations', FeatureData[NOG])],
name='Annotate orthologs against eggNOG database',
name='Annotate orthologs against eggNOG database.',
description="Apply eggnog mapper to annotate seed orthologs.",
citations=[citations["huerta_cepas_eggnog_2019"]]
)
Expand Down Expand Up @@ -830,7 +829,7 @@
output_descriptions={
'loci': "Gene coordinates files (one per MAG) listing the location of "
"each predicted gene as well as some additional scoring "
"information. ",
"information.",
'genes': "Fasta files (one per MAG) with the nucleotide sequences of "
"the predicted genes.",
'proteins': "Fasta files (one per MAG) with the protein translation "
Expand All @@ -841,7 +840,7 @@
"Gene-finding ALgorithm), a gene prediction algorithm "
"designed for improved gene structure prediction, translation "
"initiation site recognition, and reduced false positives in "
"prokaryotic genomes.",
"bacterial and archaeal genomes.",
citations=[citations["hyatt_prodigal_2010"]]
)

Expand Down Expand Up @@ -928,10 +927,11 @@
"when calculating percentages for classified reads."
},
output_descriptions={
"abundances": "Read abundances.", "taxonomy": "Linked taxonomy."
"abundances": "Read abundances.",
"taxonomy": "Linked taxonomy."
},
name="Classify reads using Kaiju.",
description="This method uses Kaiju to perform taxonomic "
"classification of NGS reads.",
"classification of DNA sequence reads.",
citations=[citations["menzel2016"]],
)

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