The core-metrics-phylogenetic
cli help docs in 2020.8.0 state:
Outputs:
--o-rarefied-table ARTIFACT FeatureTable[Frequency]
The resulting rarefied feature table. [required]
--o-faith-pd-vector ARTIFACT SampleData[AlphaDiversity]
Vector of Faith PD values by sample. [required]
--o-observed-features-vector ARTIFACT SampleData[AlphaDiversity]
Vector of Observed Features values by sample.
[required]
--o-shannon-vector ARTIFACT SampleData[AlphaDiversity]
Vector of Shannon diversity values by sample.
[required]
--o-evenness-vector ARTIFACT SampleData[AlphaDiversity]
Vector of Pielou's evenness values by sample.
[required]
--o-unweighted-unifrac-distance-matrix ARTIFACT
DistanceMatrix Matrix of unweighted UniFrac distances between
pairs of samples. [required]
--o-weighted-unifrac-distance-matrix ARTIFACT
DistanceMatrix Matrix of weighted UniFrac distances between pairs
of samples. [required]
--o-jaccard-distance-matrix ARTIFACT
DistanceMatrix Matrix of Jaccard distances between pairs of
samples. [required]
--o-bray-curtis-distance-matrix ARTIFACT
DistanceMatrix Matrix of Bray-Curtis distances between pairs of
samples. [required]
--o-unweighted-unifrac-pcoa-results ARTIFACT
PCoAResults PCoA matrix computed from unweighted UniFrac
distances between samples. [required]
--o-weighted-unifrac-pcoa-results ARTIFACT
PCoAResults PCoA matrix computed from weighted UniFrac
distances between samples. [required]
--o-jaccard-pcoa-results ARTIFACT
PCoAResults PCoA matrix computed from Jaccard distances between
samples. [required]
--o-bray-curtis-pcoa-results ARTIFACT
PCoAResults PCoA matrix computed from Bray-Curtis distances
between samples. [required]
--o-unweighted-unifrac-emperor VISUALIZATION
Emperor plot of the PCoA matrix computed from
unweighted UniFrac. [required]
--o-weighted-unifrac-emperor VISUALIZATION
Emperor plot of the PCoA matrix computed from
weighted UniFrac. [required]
--o-jaccard-emperor VISUALIZATION
Emperor plot of the PCoA matrix computed from
Jaccard. [required]
--o-bray-curtis-emperor VISUALIZATION
Emperor plot of the PCoA matrix computed from
Bray-Curtis. [required]
Why do all of these have to be required? Maybe the user doesn’t want all of that output. How about changing all of these to option, and if the user doesn’t provide a path, then that analysis isn’t done and no file is written.