read_rdml_run
Read-only
Read an instrument's RDML export - the open qPCR exchange standard, v1.0 to v1.4 - and hand back one run's contents as the same tables every other qPCR tool here takes.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| run | No | which run to read, 0-based across every experiment in the file in document order. A file routinely holds several; `summary` lists them all whatever this is set to. | |
| table | No | which table to return for the chosen run. `summary` reads the file without importing anything. The other four are exactly what the panel's four `Send to ...` buttons produce, so a value imported here and one imported there cannot differ. Values: summary (Summary - what every run in the file holds), curves (Amplification curves - Cycle,<reaction>,...), cq (Instrument Cq values - the wide Ct table plus its group column), genorm (Instrument Cq values - long Target,Sample,Cq), melt (Melting curves - Temperature,<reaction>,...), partitions (Digital PCR partition counts - Well,Sample,Target,Positives,Partitions). | summary |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| rdml_xml | Yes | the RDML document as XML text - the `rdml_data.xml` member of a `.rdml` archive, or a bare `.xml` export. Not base64 and not a file path. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| rows | Yes | data rows in `table`, excluding its header | |
| runs | Yes | every run in the file and what it holds - reactions, curves, melt curves, instrument Cq values, partition counts, the declared partition volumes, targets and samples | |
| table | Yes | the chosen run's table, as the text the matching tool's own parser takes. Empty when the run has nothing of that kind - which is a fact about the run, not a failure | |
| groups | Yes | for `cq`: one sample name per row of the Ct table, already aligned to it. The group column relative quantification needs | |
| omitted | Yes | what the import deliberately left out and why - wells whose Cq is RDML's -1 `not available`, and samples whose replicates do not square up across targets. Never padded and never zero-filled (a Ct of 0 is a fabricated measurement) | |
| version | Yes | the RDML version the file declares (1.0-1.4). The reader's behaviour differs by version and a table without it is not reproducible |