Commit af9c724e authored by mmassaviol's avatar mmassaviol
Browse files

Add yaml files describing tools commands, inputs, outputs, options, ...

parent f14542d3
{
id: deseq2,
name: DESeq2,
article: "10.1186/s13059-014-0550-8",
website: "https://bioconductor.org/packages/release/bioc/html/DESeq2.html",
git: "git clone https://git.bioconductor.org/packages/DESeq2",
description: "Differential gene expression analysis based on the negative binomial distribution. Using normalized count data.",
commands:
[
{
name: deseq2,
command: ~,
output_dir: deseq2,
inputs: [{ name: counts }],
outputs: [{ name: de_table, file: de_table.csv }, { name: RData, file: data.RData }],
options: [],
},
],
}
{
id: edger,
name: edgeR,
article: "10.18129/B9.bioc.edgeR",
website: "http://bioconductor.org/packages/release/bioc/html/edgeR.html",
git: "git clone https://git.bioconductor.org/packages/edgeR",
description: "Empirical Analysis of Digital Gene Expression Data.",
commands:
[
{
name: edger,
command: ~,
output_dir: edger,
inputs: [{ name: counts }],
outputs: [{ name: de_table }, { name: RData }],
options: [],
},
],
}
{
id: fastqc,
name: FastQC,
article: ~,
website: "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/",
git: "https://github.com/s-andrews/FastQC",
description: "A quality control tool for high throughput raw sequence data.",
commands:
[
{
name: fastqc,
command: fastqc,
output_dir: fastqc,
inputs: [{ name: reads }],
outputs: [{ name: html }, { name: zip }],
options:
[
{
name: fastqc_threads,
prefix: -t,
type: numeric,
default: 1,
min: 1,
max: NA,
step: 1,
label: "Number of threads to use",
},
],
},
],
}
{
id: kallisto,
name: kallisto,
article: "10.1038/nbt.3519",
website: "https://pachterlab.github.io/kallisto/",
git: "https://github.com/pachterlab/kallisto",
description: "kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.",
commands:
[
{
name: kallisto_index,
command: kallisto index,
output_dir: kallisto/index,
inputs:
[
{
id: kallisto_index_input,
type: text,
default: "",
label: "Address to reference fasta file",
},
],
outputs: [{ name: index }],
options: [],
},
{
name: kallisto_quant,
command: kallisto quant,
output_dir: kallisto/quant,
inputs: [{ name: index }, { name: reads }],
outputs:
[
{ name: h5, file: abundance.h5 },
{ name: counts, file: abundance.tsv },
{ name: run_info, file: run_info.json },
],
options:
[
{
name: kallisto_quant_threads,
prefix: -t,
type: numeric,
default: 1,
min: 1,
max: NA,
step: 1,
label: "Number of threads to use",
},
{
name: kallisto_quant_pe_stranded,
type: radio,
choices: [Not stranded: "", Forward Reverse: --fr-stranded, Reverse Forward: --rf-stranded],
default: "",
label: For strand specific mode choose --fr-stranded if the first read is forward and choose --rf-stranded if the first read is reverse,
},
],
},
],
}
{
id: salmon,
name: Salmon,
article: "10.1038/nmeth.4197",
website: "https://combine-lab.github.io/salmon/",
git: "https://github.com/COMBINE-lab/salmon",
description: "Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. ",
commands:
[
{
name: salmon_index,
command: salmon index,
output_dir: salmon/index,
inputs:
[
{
name: salmon_index_input,
prefix: -t,
type: text,
default: "",
label: "Address to reference fasta file",
},
],
outputs: [{name: index}],
options:
[
{
name: salmon_index_threads,
prefix: -p,
type: numeric,
default: 1,
min: 1,
max: NA,
step: 1,
label: "Number of threads to use for index creation",
},
],
},
{
name: salmon_quant,
command: salmon quant,
output_dir: salmon/quant,
inputs: [{ name: index }, { name: reads }],
outputs:
[
{ name: lib_counts, file: lib_format_counts.json },
{ name: counts, file: quant.sf },
{ name: run_info, file: cmd_info.json },
],
options:
[
{
name: salmon_quant_threads,
prefix: -t,
type: numeric,
default: 1,
min: 1,
max: NA,
step: 1,
label: "Number of threads to use",
},
],
},
],
}
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