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. This is the step every qPCR analysis starts from. Lists what each run actually holds (amplification curves, melting curves, instrument Cq values, digital-PCR partition counts with the partition volume the file declares) before anything is imported, so a run is chosen on what is in it rather than on its name. Takes the UNCOMPRESSED XML: a .rdml archive is a zip, and the tool vocabulary here has no file input.
Input Schema
TableJSON 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
TableJSON 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 |