analyze_melt_curves
Read-only
Melt curves to melting temperature, under any of THREE engines that answer different questions and none of which is a fallback for another.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| _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. | |
| engine | No | which of the three engines runs. They answer DIFFERENT questions: `plate` is the only one that produces a verdict, `vertex` the only one whose Tm is not a sampled temperature, `curve` the only one that reports peak areas. Values: plate (Plate (RDML-Python) - normalise, classify, verdicts), vertex (Vertex (MBmca diffQ) - sub-grid Tm), curve (Per curve (qpcR) - peak areas). | plate |
| _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. | |
| cut_area | No | `curve` only: drop peaks whose area is under this fraction of the largest. 0 keeps every peak, which is upstream's own default. Only applies when engine is curve. Advanced. | |
| extremum | No | `vertex` only: which extremum the melt sits at. `auto` reads each curve's direction, because upstream assumes a signal that RISES with temperature and a solution-phase melt FALLS — on which the default walks to the far end of the curve and returns a plausible-looking wrong Tm. Only applies when engine is vertex. | auto |
| resample | No | `vertex` only: resample the curve onto an even temperature grid before differentiating. Only applies when engine is vertex. Advanced. | |
| all_peaks | No | `vertex` only: report every peak the curve carries, not the dominant one alone. Only applies when engine is vertex. Advanced. | |
| melt_table | Yes | the melt table: a header row, first column the temperature and every other column one reaction's fluorescence. The same table the Melt tab takes. | |
| span_peaks | No | `curve` only: the span Friedman's super smoother uses when the peaks are called. Only applies when engine is curve. Advanced. | |
| expected_tm | No | the product's expected melting temperature, which is what turns a peak list into a verdict. Left unset, every peak is reported and none is classified - an honest absence rather than a guess. Read by the `plate` engine only, because it is the only one that classifies. In C. Only applies when engine is plate. | |
| norm_method | No | `plate` only: how each curve is normalised before it is derived. Only applies when engine is plate. Advanced. | exponential |
| peak_cutoff | No | `plate` only: the height a candidate must reach, as a percentage of the largest peak. In %. Only applies when engine is plate. Advanced. | |
| span_smooth | No | `curve` only: the smoothing span of the cubic spline fitted before the analytic derivative. Only applies when engine is curve. Advanced. | |
| fluor_source | No | `plate` only: which matrix a peak's fluorescence drop is read from — the normalised curve or the smoothed raw one. Only applies when engine is plate. Advanced. | normalised |
| expo_low_temp | No | `plate` only: low end of the window the EXPONENTIAL background is fitted over. In C. Only applies when norm_method is exponential or combined. Advanced. | |
| peak_low_temp | No | `plate` only: lowest temperature a peak is looked for at. In C. Only applies when engine is plate. Advanced. | |
| expo_high_temp | No | `plate` only: high end of the exponential fit window. In C. Only applies when norm_method is exponential or combined. Advanced. | |
| peak_high_temp | No | `plate` only: highest temperature a peak is looked for at. In C. Only applies when engine is plate. Advanced. | |
| peak_max_width | No | `plate` only: widest a peak may be before it is not read as one product. In C. Only applies when engine is plate. Advanced. | |
| window_ceiling | No | `vertex` only: the largest neighbourhood half-width the quadratic is tried at. Every width from 2 up to this is fitted and the one with the best adjusted R-squared wins, so the Tm arrives with the fit quality that chose it. Only applies when engine is vertex. | |
| true_peak_width | No | `plate` only: half-width of the window around `expected_tm` a peak must fall in to count as the product. In C. Only applies when engine is plate. Advanced. | |
| replicate_robust | No | replicate spread as median and MAD rather than mean and SD. Engine-independent: it describes the readings, so every run carries it. Advanced. | |
| replicate_percent | No | report replicate spread as a PERCENTAGE of the mean rather than in degrees. Advanced. | |
| second_derivative | No | `vertex` only: locate the inflection points of the melt (diffQ2) rather than the peak of the first derivative. Only applies when engine is vertex. Advanced. | |
| artifact_peak_width | No | `plate` only: half-width used when an extra peak is measured as an artifact. In C. Only applies when engine is plate. Advanced. | |
| bilin_low_stop_temp | No | `plate` only: end of the low seed window. In C. Only applies when norm_method is bilinear or combined. Advanced. | |
| bilin_high_stop_temp | No | `plate` only: end of the high seed window — same narrow effect as its start, for the same reproduced reason. In C. Only applies when norm_method is bilinear or combined. Advanced. | |
| bilin_low_start_temp | No | `plate` only: start of the LOW seed window the bilinear background is fitted from. In C. Only applies when norm_method is bilinear or combined. Advanced. | |
| bilin_high_start_temp | No | `plate` only: start of the high seed window. NARROWER THAN IT LOOKS, and upstream's own quirk reproduced: the high baseline scan walks a hard-coded 90-91 C seed, so this knob feeds ONLY the first exponential-free fit and moves the result far less than the low window does. The windows actually chosen come back in the result. In C. Only applies when norm_method is bilinear or combined. Advanced. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| count | Yes | how many reactions were analysed | |
| engine | Yes | which engine produced these rows, named: the three answer different questions and a Tm without its engine is not comparable | |
| meanTm | Yes | mean dominant Tm over the reactions that produced a peak | |
| noPeak | Yes | reactions with no melting peak at all: a reaction that did not amplify, reported rather than dropped | |
| targets | Yes | `plate` only: per target, the reactions that contributed a product peak and their averaged Tm against the expected one. Empty for `vertex` and `curve` | |
| meltPlot | Yes | the melt curves as read from the table, one line per reaction, fluorescence against temperature. Every engine reads this same input | |
| reactions | Yes | one row per reaction, in the shape the CHOSEN engine reports: `plate` gives peaks plus a verdict, `vertex` gives the sub-grid Tm with the adjusted R-squared that chose its window, `curve` gives every peak with its area | |
| classified | Yes | whether the peaks were classified, and why not when they were not — including 'this engine does not classify', which is a property of the choice and not a failure | |
| derivativePlot | Yes | `plate` only: −dF/dT of each reaction after normalisation and smoothing, the curve its peaks are called on, one line per reaction. Null for `vertex` and `curve`, which fit near the extremum and report no whole derivative | |
| replicateSpread | Yes | location and deviation per temperature per target, from the plate's own replicates. Engine-independent: it describes the readings, not the method, so every run carries it |