CI
dcf61f0448
Build pipeline: viash-hub.craftbox.main-q4xsw
Source commit: a80fa3ef02
Source message: `move_files_to_directory`: add support for preserving symbolic links (#13)
116 lines
4.5 KiB
JSON
116 lines
4.5 KiB
JSON
{
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"$schema": "https://json-schema.org/draft/2020-12/schema",
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"title": "csv2fasta",
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"description": "Convert two columns from a CSV file to FASTA entries. The CSV file can\ncontain an optional header and each row (other than the header) becomes\na single FASTA record. One of the two columns will be used as the names\nfor the FASTA entries, while the other become the sequences. The sequences\ncolumn must only contain characters that are valid IUPAC notation for \nnucleotides or a group thereof (wildcard characters).\n",
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"type": "object",
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"$defs": {
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"inputs": {
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"title": "Inputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"input": {
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"type": "string",
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"format": "path",
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"exists": true,
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"description": "CSV file to be processed.",
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"help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"barcodes.csv\"`. "
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},
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"header": {
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"type": "boolean",
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"description": "Parse the first line of the CSV file as a header.\n",
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"help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
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"default": false
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}
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}
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},
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"outputs": {
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"title": "Outputs",
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"type": "object",
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"description": "No description",
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"properties": {
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"output": {
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"type": "string",
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"format": "path",
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"description": "Output fasta file.",
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"help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.fasta\"`, direction: `output`, example: `\"barcodes.fasta\"`. ",
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"default": "$id.$key.output.fasta"
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}
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}
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},
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"csv dialect options": {
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"title": "CSV dialect options",
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"type": "object",
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"description": "Options that can be used to override the automatically detected\ndialect of the CSV file.\n",
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"properties": {
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"delimiter": {
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"type": "string",
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"description": "Overwrite the column delimiter character.\n",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"quote_character": {
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"type": "string",
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"description": "Overwrite the character used to denote the start and end of a quoted item.\n",
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"help_text": "Type: `string`, multiple: `False`. "
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}
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}
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},
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"csv column arguments": {
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"title": "CSV column arguments",
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"type": "object",
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"description": "Parameters for the selection of columns from the CSV file.\nOnly required when your CSV file contains more than 2 columns,\notherwise the first column will be used for the FASTA header\nand the second for the FASTA nucleotide sequences. This default\ncan still be overwritten by using the options below.\n",
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"properties": {
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"sequence_column": {
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"type": "string",
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"description": "Name of the column containing the sequences",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"name_column": {
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"type": "string",
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"description": "Name of the column describing the FASTA headers",
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"help_text": "Type: `string`, multiple: `False`. "
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},
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"sequence_column_index": {
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"type": "integer",
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"description": "Index of the column to use as the FASTA sequences, counter from the left and\nstarting from 0",
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"help_text": "Type: `integer`, multiple: `False`. "
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},
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"name_column_index": {
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"type": "integer",
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"description": "Index of the column to use as the FASTA headers, counter from the left and\nstarting from 0",
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"help_text": "Type: `integer`, multiple: `False`. "
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}
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}
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},
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"nextflow input-output arguments": {
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"title": "Nextflow input-output arguments",
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"type": "object",
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"description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
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"properties": {
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"publish_dir": {
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"type": "string",
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"description": "Path to an output directory.",
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"help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
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}
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}
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}
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},
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"allOf": [
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{
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"$ref": "#/$defs/inputs"
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},
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{
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"$ref": "#/$defs/outputs"
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},
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{
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"$ref": "#/$defs/csv dialect options"
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},
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{
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"$ref": "#/$defs/csv column arguments"
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},
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{
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"$ref": "#/$defs/nextflow input-output arguments"
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}
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]
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}
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