Add ampvis2 export otu #6748
Add ampvis2 export otu #6748
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| <output name="otu_short" value="output_otu_short.tsv" ftype="tabular" /> | ||
| <output name="tax" value="output_otu_taxonomy_mapping.tsv" ftype="tabular" /> | ||
| <output name="meta" value="output_metadata.tsv" ftype="tabular" /> | ||
| <output name="phyloseq" value="output_phyloseq.rds" ftype="phyloseq" compare="sim_size" delta_frac="0.1"/> |
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Use a has_size content assertion and remove output_phyloseq.rds
| <data name="otu_long" format="tabular" label="${tool.name}: Long OTU" /> | ||
| <data name="otu_short" format="tabular" label="${tool.name}: Short OTU"/> | ||
| <data name="tax" format="tabular" label="${tool.name}: Taxonomy mapping" /> | ||
| <data name="meta" format="tabular" label="${tool.name}: Metadata mapping" /> | ||
| <data name="phyloseq" format="phyloseq" label="${tool.name}: Phyloseq object" /> |
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Can we make all of them optional? Controlled by a single select (by using min="1" we can enforce that at least one option is selected).
| SampleID Plant Date Year Period V6 | ||
| 16SAMP-747 16SAMP-747 Aalborg East 2010-02-04 2010 Winter |
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Somehow we get an additional V6 in the column header. I guess you need to disable row names in the output.
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When trying to fix this I discovered, that the original input to create that ampvis2 object actually only has 4 columns (https://github.com/galaxyproject/tools-iuc/blob/main/tools/ampvis2/test-data/AalborgWWTPs.tsv), even when ampvis adds the first unnamed column as sampleID, this is pretty strange ... but seems to lead to this issue when exporting.
Plant Date Year Period
16SAMP-747 16SAMP-747 Aalborg East 2010-02-04 2010 Winter
When exporting using e.g. the subset it works.
Co-authored-by: M Bernt <[email protected]>
FOR CONTRIBUTOR:
ping @bernt-matthias
pretty useful for downstream analysis after subsampling