Export ASAP

Version: 1.0.0

Commit Hash: 13f1edd43b49ea7d43246b751cad4477c505a310

Author:

Category: utilities

Exports ASAP files from an SDRF file.

Install with Cauldron get_app
README

Export ASAP

Installation

⬇️ Click here to install in Cauldron (requires Cauldron to be running)

Repository: https://github.com/noatgnu/export_asap_plugin

Manual installation:

  1. Open Cauldron
  2. Go to Plugins → Install from Repository
  3. Paste: https://github.com/noatgnu/export_asap_plugin
  4. Click Install

ID: export-asap
Version: 1.0.0
Category: utilities
Author:

Description

Exports ASAP files from an SDRF file.

Runtime

  • Type: python
  • Script: export_asap.py

Inputs

Name Label Type Required Default Visibility
sdrf_file SDRF File file Yes - Always visible
asap_team_name ASAP Team Name text No Alessi Always visible
asap_lab_name ASAP Lab Name text No Dario Alessi Always visible
pi_full_name PI Full Name text No Dario R. Alessi Always visible
project_name Project Name text No Always visible
project_description Project Description text No Always visible
dataset_title Dataset Title text No Always visible
dataset_description Dataset Description text No Always visible
dataset_name Dataset Name text No Always visible
pi_email PI Email text No Always visible
contributor_names Contributor Names text No Always visible
submitter_name Submitter Name text No Always visible
submitter_email Submitter Email text No Always visible
asap_grant_id ASAP Grant ID text No Always visible
other_funding_source Other Funding Source text No Always visible
publication_doi Publication DOI text No Always visible
publication_pmid Publication PMID text No Always visible
number_samples Number of Samples text No Always visible
sample_types Sample Types text No Always visible
types_of_samples Types of Samples text No Always visible
metadata_tables Metadata Tables text No SDRF.tsv Always visible
dua_version DUA Version text No Always visible
pi_orcid PI ORCID text No Always visible
pi_google_scholar_id PI Google Scholar ID text No Always visible
preprocessing_references Preprocessing References text No Always visible
metadata_version_date Metadata Version Date text No Always visible
alternate_dataset_id Alternate Dataset ID text No Always visible

Input Details

SDRF File (sdrf_file)

The input SDRF file in .tsv format.

ASAP Team Name (asap_team_name)

Name of the ASAP team.

ASAP Lab Name (asap_lab_name)

Name of the ASAP lab.

PI Full Name (pi_full_name)

Full name of the Principal Investigator.

Project Name (project_name)

Project Description (project_description)

Dataset Title (dataset_title)

Dataset Description (dataset_description)

Dataset Name (dataset_name)

PI Email (pi_email)

Contributor Names (contributor_names)

Submitter Name (submitter_name)

Submitter Email (submitter_email)

ASAP Grant ID (asap_grant_id)

Other Funding Source (other_funding_source)

Publication DOI (publication_doi)

Publication PMID (publication_pmid)

Number of Samples (number_samples)

Sample Types (sample_types)

Types of Samples (types_of_samples)

Metadata Tables (metadata_tables)

DUA Version (dua_version)

PI ORCID (pi_orcid)

PI Google Scholar ID (pi_google_scholar_id)

Preprocessing References (preprocessing_references)

Metadata Version Date (metadata_version_date)

Alternate Dataset ID (alternate_dataset_id)

Outputs

Name File Type Format Description
output_dir .

Requirements

  • Python: >=3.8
  • Additional Packages:
  • sdrf_pipelines
  • pandas

Usage

Via UI

  1. Navigate to utilities → Export ASAP
  2. Fill in the required inputs
  3. Click Run Analysis

Via Plugin System

const jobId = await pluginService.executePlugin('export-asap', {
  // Add parameters here
});