{"links":{"first":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/2.0/tools?format=json&page=1","last":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/2.0/tools?format=json&page=1","next":null,"prev":null},"data":[{"type":"pipeline-tools","id":"Biopython","attributes":{"tool-name":"Biopython","description":"A set of freely available tools for biological computation written in Python.","web-link":"http://biopython.org/wiki/Biopython","version":"1.65","exe-command":"N/A","configuration-file":null,"notes":null},"relationships":{"pipelines":{"data":[{"type":"pipelines","id":"2.0","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/2.0?format=json"}},{"type":"pipelines","id":"3.0","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/3.0?format=json"}},{"type":"pipelines","id":"4.0","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/4.0?format=json"}},{"type":"pipelines","id":"4.1","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/4.1?format=json"}}]}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/Biopython/1.65?format=json"}},{"type":"pipeline-tools","id":"FragGeneScan","attributes":{"tool-name":"FragGeneScan","description":"An application for finding fragmented genes in short reads.","web-link":"http://omics.informatics.indiana.edu/FragGeneScan/","version":"1.15","exe-command":"./FragGeneScan -s {0} -o {0}_CDS -w 0 -t 454_10","configuration-file":null,"notes":null},"relationships":{"pipelines":{"data":[{"type":"pipelines","id":"1.0","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/1.0?format=json"}},{"type":"pipelines","id":"2.0","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/2.0?format=json"}}]}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/FragGeneScan/1.15?format=json"}},{"type":"pipeline-tools","id":"InterProScan","attributes":{"tool-name":"InterProScan","description":"A sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource.","web-link":"https://github.com/ebi-pf-team/interproscan/wiki","version":"5.9-50.0","exe-command":"./interproscan.sh --appl PfamA,TIGRFAM-10.1,PRINTS,PrositePatterns,Gene3d -goterms -o {1}_out.tsv -i {1}","configuration-file":null,"notes":null},"relationships":{"pipelines":{"data":[{"type":"pipelines","id":"2.0","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/2.0?format=json"}}]}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/InterProScan/5.9-50.0?format=json"}},{"type":"pipeline-tools","id":"QIIME","attributes":{"tool-name":"QIIME","description":"An open-source bioinformatics pipeline for performing taxonomic analysis from raw DNA sequencing data.","web-link":"http://qiime.org/","version":"1.9.0","exe-command":"./qiime190Wrapper.sh  {1} {2} {3}","configuration-file":null,"notes":null},"relationships":{"pipelines":{"data":[{"type":"pipelines","id":"2.0","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/2.0?format=json"}}]}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/QIIME/1.9.0?format=json"}},{"type":"pipeline-tools","id":"rRNASelector","attributes":{"tool-name":"rRNASelector","description":"A computer program for selecting ribosomal RNA encoding sequences from metagenomic and metatranscriptomic shotgun libraries.","web-link":"http://www.ezbiocloud.net/sw/rrnaselector","version":"1.0.1","exe-command":"./pipelineDetectRRNA.sh {1} {2} {3}","configuration-file":null,"notes":null},"relationships":{"pipelines":{"data":[{"type":"pipelines","id":"2.0","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/2.0?format=json"}}]}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/rRNASelector/1.0.1?format=json"}},{"type":"pipeline-tools","id":"Trimmomatic","attributes":{"tool-name":"Trimmomatic","description":"A flexible read trimming tool.","web-link":"http://www.usadellab.org/cms/?page=trimmomatic","version":"0.32","exe-command":"java -classpath {0}/Trimmomatic-0.32/trimmomatic-0.32.jar org.usadellab.trimmomatic.TrimmomaticSE  -phred33 {1} {2} LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15","configuration-file":null,"notes":null},"relationships":{"pipelines":{"data":[{"type":"pipelines","id":"1.0","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/1.0?format=json"}},{"type":"pipelines","id":"2.0","links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/2.0?format=json"}}]}},"links":{"self":"https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/Trimmomatic/0.32?format=json"}}],"meta":{"pagination":{"page":1,"pages":1,"count":6}}}