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#!/bin/bash
#
# ./makelist.sh
#
set -eu

#
# Input tables
#

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added: <file:///data/rnaseq-readcount/rnaseq-readcount.cwl> <https://w3id.org/cwl/cwl#Workflow/steps> <file:///data/rnaseq-readcount/rnaseq-readcount.cwl#pfastq_dump> .
added: <file:///data/rnaseq-readcount/rnaseq-readcount.cwl> <https://w3id.org/cwl/cwl#outputs> <file:///data/rnaseq-readcount/rnaseq-readcount.cwl#STAR_logfiles> .
added: <file:///data/rnaseq-readcount/rnaseq-readcount.cwl> <https://w3id.org/cwl/cwl#outputs> <file:///data/rnaseq-readcount/rnaseq-readcount.cwl#STAR_readsPerGene> .
added: <file:///data/rnaseq-readcount/rnaseq-readcount.cwl> <https://w3id.org/cwl/cwl#outputs> <file:///data/rnaseq-readcount/rnaseq-readcount.cwl#rsem_genes_result> .
added: <file:///data/rnaseq-readcount/rnaseq-readcount.cwl> <https://w3id.org/cwl/cwl#outputs> <file:///data/rnaseq-readcount/rnaseq-readcount.cwl#rsem_isoforms_result> .
added: <file:///data/rnaseq-readcount/pfastq_dump.cwl> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <https://w3id.org/cwl/cwl#CommandLineTool> .
added: <file:///data/rnaseq-readco

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# Calculate average throughput for long read sequencing data

PREFIX sos: <http://purl.jp/bio/01/quanto/ontology/sos#>
PREFIX quanto: <http://purl.jp/bio/01/quanto/resource/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX pav: <http://purl.org/pav/>

SELECT (AVG(?total_sequences AS ?average_throughput))
FROM <http://quanto.dbcls.jp>

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# Retrieve top 50 high-throughput sequencing runs with filtering by base call quality and read length
PREFIX sos: <http://purl.jp/bio/01/quanto/ontology/sos#>
PREFIX quanto: <http://purl.jp/bio/01/quanto/resource/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX pav: <http://purl.org/pav/>

SELECT ?id ?insdcId ?median_bc_quality ?total_sequences ?median_seq_length
FROM <http://quanto.dbcls.jp>
WHERE {

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#!/bin/bash
set -eu

USER_DIR="/home/galaxy"

if [[ -z `sudo ls / 2>/dev/null` ]]; then
  echo "Permission denied: you have to be granted sudo privileges. Quit"
  exit 1
fi

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Application Name:	ZOOMA (Automatic Ontology Mapper)
Version:	2.0
Run at:	01:23.20, 16.12.16
Run from:	http://www.ebi.ac.uk/fgpt/zooma


PROPERTY TYPE	PROPERTY VALUE	ONTOLOGY TERM LABEL(S)	ONTOLOGY TERM SYNONYM(S)	CONFIDENCE	ONTOLOGY TERM(S)	ONTOLOGY(S)	SOURCE(S)	STUDY
[NO TYPE]	0-12h embryos	N/A	N/A	Did not map	N/A	N/A	N/A	[UNKNOWN EXPERIMENTS]
[NO TYPE]	0-16h embryos	N/A	N/A	Did not map	N/A	N/A	N/A	[UNKNOWN EXPERIMENTS]
[NO TYPE]	0-24h embryos	N/A	N/A	Did not map	N/A	N/A	N/A	[UNKNOWN EXPERIMENTS]

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require 'set'

class Table
  def initialize(table_path, tax_name, tax_rank)
    @table = load_table(table_path, "\t")
    @names  = load_table(tax_name, "\t|\t").to_set
    @ranks  = load_table(tax_rank, "\t|\t").to_set
  end
  
  def load_table(path, chr)

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@prefix dcterms: <http://purl.org/dc/terms/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix pav: <http://purl.org/pav/> .
@prefix quanto: <http://purl.jp/bio/01/quanto/resource/> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix sos: <http://purl.jp/bio/01/quanto/ontology/sos#> .
@prefix uo: <http://purl.obolibrary.org/obo/> .

quanto:DRR000001_1_fastqc a sos:SequenceStatisticsReport;

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FROM ubuntu:trusty

RUN apt-get -y update && \
    apt-get install -y \
    wget \
    make \
    libncurses5-dev \
    libncursesw5-dev \
    libboost-all-dev \
    g++ && \

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How to describe experimental protocol in EPL format

This document is not yet done. Please contact [email protected] for more details.

What is this

This is a guideline for biologists to translate the experimental protocols written in natural language to the Experimental Protocol Language (EPL) format.

How it works