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  • This step of the ARMS IJI workflow does the following: - Input: the OTU tables from the previous step (running the omics pipeline), containing taxa (usually genus or species names) obtained from the databases used by the pipeline; - Check: using the WoRMS taxon match webservice to check for the WoRMS match to those taxa; - Output: the WoRMS match (yes or not) and, if matched, the scientific name and aphiaID. It represents the Step 7 of the ARMS Workflow within the Internal Joint Initiative.

  • This service represents the Step 5.3 of the ARMS Workflow within the Internal Joint Initiative. It can be run optionally on the fasta files produced by Step 5.2 (PEMA Runner) and produces an all_sequences_grouped_fasta_output.csv file as output.

  • This step of the ARMS IJI workflow does the following: - Input: the output from the previous step (running a taxon check on the input species names using the WoRMS taxon checker); - Input: geographical locations for the sample(s) that those species were found at; - Check: using the WRIMS taxon match webservice to check the known distribution of the species; - Output: information about whether the species are alien or native to the location they were found at. It represents the Step 8 of the ARMS Workflow within the Internal Joint Initiative.

  • This service aims at creating an OTU table with species information that can be processed by WoRMS and WRIMS (steps 7 and 8). It represents the Step 6 of the ARMS Workflow within the Internal Joint Initiative.

  • This service aims to download the sequences files (fasq files) that have been choosen in Step 4 (ARMS Choose and Parameterize) in order to run PEMA. It represents the Step 5.1 of the ARMS Workflow within the Internal Joint Initiative.

  • This service aims to uploading a local file in the ARMS validation case. It represents the Step 2 of the ARMS Workflow within the Internal Joint Initiative.

  • This service aims at running PEMA on all the sequences from the samples selected in Step 4 (ARMS Choose and Parameterize) of the ARMS workflow. It additionally requires a parameter file (a tsv file). The service can take some hours to run. It represents the Step 5.2 of the ARMS Workflow within the Internal Joint Initiative.

  • This service aims to reformat and produce final output in variuos formats for human and machine2machine reading. It represents the Step 9 of the ARMS Workflow within the Internal Joint Initiative.

  • This service allows to choose which column of the MasterARMS file contains the specific data to process. Moreover, it permits to provide additional files or arguments as parameters. It represents the Step 4 of the ARMS Workflow within the Internal Joint Initiative.

  • This service allows to filter the list of samples in the MasterARMS csv file on date range (start and end date in ISO format) and geographic location (lat and lon in decimal degrees). Moreover, also the selection of specific samples is permitted. It represents the Step 3 of the ARMS Workflow within the Internal Joint Initiative.