Export a preset file given the preset name or source file and a set of mix-ins
This command can help to understand structure of preset or compare presets.
Exported file may be a starting point for writing custom preset.
Command line options
``` mixcr exportPreset (--preset-name
[--force-overwrite]
[--no-warnings]
[--verbose]
[--help]
# mix-ins
[--add-step <step>]
[--remove-step <step>]
[-s <species>]
[-b <library>]
[--split-by-sample]
[--dont-split-by-sample]
[--sample-table sample_table.tsv]
[--dna]
[--rna]
[--floating-left-alignment-boundary [<anchor_point>]]
[--rigid-left-alignment-boundary [<anchor_point>]]
[--floating-right-alignment-boundary (<gene_type>|<anchor_point>)]
[--rigid-right-alignment-boundary [(<gene_type>|<anchor_point>)]]
[--tag-pattern <pattern>]
[--keep-non-CDR3-alignments]
[--drop-non-CDR3-alignments]
[--limit-input <n>]
[--assemble-clonotypes-by <gene_features>]
[--split-clones-by <gene_type>]...
[--dont-split-clones-by <gene_type>]...
[--assemble-contigs-by <gene_features>]
[--impute-germline-on-export]
[--dont-impute-germline-on-export]
[--prepend-export-clones-field <field> [<param>...]]...
[--append-export-clones-field <field> [<param>...]]...
[--prepend-export-alignments-field <field> [<param>...]]...
[--append-export-alignments-field <field> [<param>...]]...
[--add-export-clone-table-splitting <(geneLabel|tag):key>]
[--reset-export-clone-table-splitting]
[--add-export-clone-grouping <(geneLabel|tag):key>]
[--reset-export-clone-grouping]
[-M <key=value>]...
# output
[preset_file.(yaml|yml)]
```
[preset_file.(yaml|yml)]- Path where to write preset yaml file. Will write to output if omitted.
--preset-name <preset>- Preset name to export (see complete list of available presets).
--mixcr-file <input.(vdjca|clns|clna)>- File that was processed by MiXCR.
--no-validation- Don't validate preset before export.
-f, --force-overwrite- Force overwrite of output file(s).
-nw, --no-warnings- Suppress all warning messages.
--verbose- Verbose messages.
-h, --help- Show this help message and exit.
In addition to these parameters, any of the available mix-in options may be additionally specify at exportPreset.
Examples
```shell
mixcr exportPreset --mixcr-file result.vdjca preset.yaml ```
Result is preset file used to process result.vdjca. The same may be applied to *.clns or *.clna files.
```shell
mixcr exportPreset --preset-name 10x-vdj-bcr preset.yaml ```
Result is preset file of 10x-vdj-bcr preset.
```shell
mixcr exportPreset --preset-name generic-tcr-amplicon --species hs \ --dna \ --floating-left-alignment-boundary \ --floating-right-alignment-boundary J \ preset.yaml ```
Result is generic-tcr-amplicon preset with all required mixins set.
```shell
mixcr exportPreset --preset-name generic-tcr-amplicon \ --no-validation \ preset.yaml ```
Result is generic-tcr-amplicon preset without some required mixins. Useful for comparing presets or writing custom preset.
```shell
diff \ <(mixcr exportPreset --preset-name 10x-vdj-bcr) \ <(mixcr exportPreset --preset-name 10x-vdj-tcr) ```
Comparing two presets between each other. Alternatively, one can export them in separate files and use some other tool for comparison.