HTTP 200 OK
Allow: GET, HEAD, OPTIONS
Content-Type: application/json
Vary: Accept
{
"links": {
"first": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/4.1/tools?format=api&page=1",
"last": "https://www.ebi.ac.uk/metagenomics/api/v1/pipelines/4.1/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": "cmsearch deoverlap script",
"attributes": {
"tool-name": "cmsearch deoverlap script",
"description": "A tool, which removes lower scoring overlaps from cmsearch --tblout files.",
"web-link": "https://github.com/nawrockie/cmsearch_tblout_deoverlap",
"version": "0.01",
"exe-command": "./cmsearch_deoverlap.pl --clanin <claninfo-file> <matches-file>",
"configuration-file": null,
"notes": null
},
"relationships": {
"pipelines": {
"data": [
{
"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/cmsearch%20deoverlap%20script/0.01?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": "Infernal",
"attributes": {
"tool-name": "Infernal",
"description": "Infernal (\"INFERence of RNA ALignment\") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.",
"web-link": "http://eddylab.org/infernal/",
"version": "1.1.2",
"exe-command": "../infernal-1.1.2/src/cmsearch --hmmonly --noali --cut_ga --cpu 4 --tblout {1} -Z 1000 -o {2} {3} {4}",
"configuration-file": null,
"notes": null
},
"relationships": {
"pipelines": {
"data": [
{
"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/Infernal/1.1.2?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": "5.25-64.0",
"exe-command": "./interproscan.sh -dp --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": "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/InterProScan/5.25-64.0?format=api"
}
},
{
"type": "pipeline-tools",
"id": "MAPseq",
"attributes": {
"tool-name": "MAPseq",
"description": "MAPseq is a set of fast and accurate sequence read classification tools designed to assign taxonomy and OTU classifications to ribosomal RNA sequences.",
"web-link": "https://github.com/jfmrod/MAPseq/",
"version": "1.2.2",
"exe-command": "./mapseq -nthreads 1 -outfmt simple {1} <customref.fasta> <customref.tax>",
"configuration-file": null,
"notes": null
},
"relationships": {
"pipelines": {
"data": [
{
"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/MAPseq/1.2.2?format=api"
}
},
{
"type": "pipeline-tools",
"id": "Prodigal",
"attributes": {
"tool-name": "Prodigal",
"description": "Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program.",
"web-link": "https://github.com/hyattpd/prodigal/wiki",
"version": "2.6.3",
"exe-command": "./prodigal -i {0} -o {1} -f sco -d {1}.ffn -a {1}.faa",
"configuration-file": null,
"notes": null
},
"relationships": {
"pipelines": {
"data": [
{
"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/Prodigal/2.6.3?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": "1.2",
"exe-command": "?",
"configuration-file": null,
"notes": null
},
"relationships": {
"pipelines": {
"data": [
{
"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/SeqPrep/1.2?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": 9
}
}
}