HTTP 200 OK
Allow: GET, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"links": {
"first": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/3.0/tools?format=api&page=1",
"last": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/3.0/tools?format=api&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=api"
}
},
{
"type": "pipelines",
"id": "3.0",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/3.0?format=api"
}
},
{
"type": "pipelines",
"id": "4.0",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/4.0?format=api"
}
},
{
"type": "pipelines",
"id": "4.1",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/4.1?format=api"
}
}
]
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/Biopython/1.65?format=api"
}
},
{
"type": "pipeline-tools",
"id": "FragGeneScan",
"attributes": {
"tool-name": "FragGeneScan",
"description": "An application for finding (fragmented) genes in short reads.",
"web-link": "https://sourceforge.net/projects/fraggenescan/",
"version": "1.20",
"exe-command": "./FragGeneScan -s {1} -o {1}_CDS -w 0 -t illumina_5 -p 8",
"configuration-file": null,
"notes": null
},
"relationships": {
"pipelines": {
"data": [
{
"type": "pipelines",
"id": "3.0",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/3.0?format=api"
}
},
{
"type": "pipelines",
"id": "4.0",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/4.0?format=api"
}
},
{
"type": "pipelines",
"id": "4.1",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/4.1?format=api"
}
}
]
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/FragGeneScan/1.20?format=api"
}
},
{
"type": "pipeline-tools",
"id": "HMMER",
"attributes": {
"tool-name": "HMMER",
"description": "A computer program for biosequence analysis using profile hidden Markov models.",
"web-link": "http://hmmer.org",
"version": "v3.1b1",
"exe-command": "./nhmmer --tblout $outpath/${file}_tRNAselect.txt --cpu 4 -T 20 tRNA.hmm $outpath/${file}.fna > /dev/null",
"configuration-file": null,
"notes": null
},
"relationships": {
"pipelines": {
"data": [
{
"type": "pipelines",
"id": "3.0",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/3.0?format=api"
}
}
]
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/HMMER/v3.1b1?format=api"
}
},
{
"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": "5.19-58.0",
"exe-command": "./interproscan.sh --appl PfamA,TIGRFAM,PRINTS,PrositePatterns,Gene3d --goterms --pathways -f tsv -o {1}_out.tsv -i {1}",
"configuration-file": null,
"notes": null
},
"relationships": {
"pipelines": {
"data": [
{
"type": "pipelines",
"id": "3.0",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/3.0?format=api"
}
}
]
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/InterProScan/5.19-58.0?format=api"
}
},
{
"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": "1.9.1",
"exe-command": "./qiime-1.9.1-wrapper.sh {1} {2} {3} {4}",
"configuration-file": null,
"notes": null
},
"relationships": {
"pipelines": {
"data": [
{
"type": "pipelines",
"id": "3.0",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/3.0?format=api"
}
}
]
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/QIIME/1.9.1?format=api"
}
},
{
"type": "pipeline-tools",
"id": "SeqPrep",
"attributes": {
"tool-name": "SeqPrep",
"description": "A program to merge paired end Illumina reads that are overlapping into a single longer read.",
"web-link": "https://github.com/jstjohn/SeqPrep",
"version": "1.1",
"exe-command": "?",
"configuration-file": null,
"notes": null
},
"relationships": {
"pipelines": {
"data": [
{
"type": "pipelines",
"id": "3.0",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/3.0?format=api"
}
},
{
"type": "pipelines",
"id": "4.0",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/4.0?format=api"
}
}
]
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/SeqPrep/1.1?format=api"
}
},
{
"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": "0.35",
"exe-command": "java -classpath {0}/Trimmomatic-0.35/trimmomatic-0.35.jar org.usadellab.trimmomatic.TrimmomaticSE -threads 8 -phred33 {1} {2} LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15",
"configuration-file": null,
"notes": null
},
"relationships": {
"pipelines": {
"data": [
{
"type": "pipelines",
"id": "3.0",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/3.0?format=api"
}
},
{
"type": "pipelines",
"id": "4.0",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/4.0?format=api"
}
},
{
"type": "pipelines",
"id": "4.1",
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/4.1?format=api"
}
}
]
}
},
"links": {
"self": "https://www.ebi.ac.uk/metagenomics/api/v1/pipeline-tools/Trimmomatic/0.35?format=api"
}
}
],
"meta": {
"pagination": {
"page": 1,
"pages": 1,
"count": 7
}
}
}