diff --git a/ro/Galaxy-wfdesc.rdf b/ro/Galaxy-wfdesc.rdf
new file mode 100644
index 0000000..a0a7329
--- /dev/null
+++ b/ro/Galaxy-wfdesc.rdf
@@ -0,0 +1,157 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+]>
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+ Galaxy workflow for reproducing Table 2 of SOAPdenovo paper
+ Galaxy workflow for reproducing Table 2 of SOAPdenovo paper
+ Galaxy workflow for reproducing Table 2 of SOAPdenovo paper
+
+ Galaxy workflow for reproducing Table 2 of SOAPdenovo paper
+
+
+
+
+
+
+
+
+ Workflow input file for KmerFreq AR
+
+
+
+
+
+ KmerFreq AR/Library1/Forward FASTQ file
+
+
+
+
+
+
+
+ Workflow input file for KmerFreq AR
+
+
+
+
+
+ KmerFreq AR/Library1/Reverse FASTQ file
+
+
+
+
+
+
+
+
+ Workflow input file for SOAPdenovo2
+
+
+
+
+
+ SOAPdenovo2/Library2/Forward FASTQ file
+
+
+
+
+
+
+
+ Workflow input file for SOAPdenovo2
+ TODO:Upload and share the data
+
+
+
+
+
+ SOAPdenovo2/Library2/Reverse FASTQ file
+
+
+
+
+
+
+
+
+ Workflow input file for GAGE/Reference genome file in FASTA format
+
+
+
+
+
+ GAGE/Reference genome file in FASTA format
+
+
+
+
+
+
+
+ Workflow output file
+
+
+
+
+
+
+
diff --git a/ro/NanoStm/nanopub1.trig b/ro/NanoStm/nanopub1.trig
new file mode 100644
index 0000000..d473242
--- /dev/null
+++ b/ro/NanoStm/nanopub1.trig
@@ -0,0 +1,69 @@
+@prefix this: .
+@prefix rdf: .
+@prefix rdfs: .
+@prefix rdfg: .
+@prefix xsd: .
+@prefix owl: .
+@prefix dc: .
+@prefix pav: .
+@prefix np: .
+
+ {
+ this: np:hasProvenance ;
+ a np:Nanopublication ;
+ np:hasPublicationInfo ;
+ np:hasAssertion .
+}
+
+ {
+ .
+
+ .
+
+ rdf: .
+
+ rdf: .
+
+ rdf: .
+
+ .
+
+ .
+
+ .
+
+ rdf: .
+
+ rdf: .
+
+ rdf: ;
+ .
+
+ .
+}
+
+ {
+ .
+
+ .
+
+ rdf: .
+
+ .
+
+ .
+
+ .
+
+ rdf: .
+
+ .
+}
+
+ {
+ > dc:created > ;
+ dc:rightsHolder > ;
+ dc:bibliographicCitation ;
+ dc:creator , ;
+ dc:hasVersion > .
+}
diff --git a/ro/Outputs/gage.out.Tabular b/ro/Outputs/gage.out.Tabular
new file mode 100644
index 0000000..6c34a79
--- /dev/null
+++ b/ro/Outputs/gage.out.Tabular
@@ -0,0 +1 @@
+80 98.6 25 71.5 38 1086 2 1078
diff --git a/ro/Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga b/ro/Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga
new file mode 100644
index 0000000..72eb545
--- /dev/null
+++ b/ro/Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga
@@ -0,0 +1,389 @@
+{
+ "a_galaxy_workflow": "true",
+ "annotation": "",
+ "format-version": "0.1",
+ "name": "Workflow constructed from history 'reproduce s.aureus pipeline'",
+ "steps": {
+ "0": {
+ "annotation": "",
+ "id": 0,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 10,
+ "top": 10
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": []
+ },
+ "1": {
+ "annotation": "",
+ "id": 1,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 10,
+ "top": 130
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": []
+ },
+ "2": {
+ "annotation": "",
+ "id": 2,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 10,
+ "top": 250
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": []
+ },
+ "3": {
+ "annotation": "",
+ "id": 3,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 10,
+ "top": 370
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": []
+ },
+ "4": {
+ "annotation": "",
+ "id": 4,
+ "input_connections": {},
+ "inputs": [
+ {
+ "description": "",
+ "name": "Input Dataset"
+ }
+ ],
+ "name": "Input dataset",
+ "outputs": [],
+ "position": {
+ "left": 10,
+ "top": 490
+ },
+ "tool_errors": null,
+ "tool_id": null,
+ "tool_state": "{\"name\": \"Input Dataset\"}",
+ "tool_version": null,
+ "type": "data_input",
+ "user_outputs": []
+ },
+ "5": {
+ "annotation": "",
+ "id": 5,
+ "input_connections": {
+ "data_format|libraries_0|input1": {
+ "id": 0,
+ "output_name": "output"
+ },
+ "data_format|libraries_0|input2": {
+ "id": 1,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "name": "KmerFreq AR",
+ "outputs": [
+ {
+ "name": "filelist",
+ "type": "Tabular"
+ },
+ {
+ "name": "stat",
+ "type": "Tabular"
+ },
+ {
+ "name": "cz_len",
+ "type": "Tabular"
+ },
+ {
+ "name": "cz",
+ "type": "Tabular"
+ },
+ {
+ "name": "genome_estimate",
+ "type": "Tabular"
+ },
+ {
+ "name": "space_stat",
+ "type": "Tabular"
+ },
+ {
+ "name": "space_cz_len",
+ "type": "Tabular"
+ },
+ {
+ "name": "space_cz",
+ "type": "Tabular"
+ },
+ {
+ "name": "space_genome_estimate",
+ "type": "Tabular"
+ }
+ ],
+ "position": {
+ "left": 230,
+ "top": 10
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "kmerfreq_ar",
+ "tool_state": "{\"space_consecutive_settings\": \"{\\\"min_precision_kmer_rate\\\": \\\"-1\\\", \\\"ascii_shift\\\": \\\"33\\\", \\\"__current_case__\\\": 0, \\\"space_consecutive_settings_type\\\": \\\"consecutive\\\", \\\"use_num_bases\\\": \\\"\\\", \\\"kmer_size\\\": \\\"17\\\", \\\"output_depth\\\": \\\"1\\\"}\", \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist-232ef8122d54/tool-data/shared/ucsc/chrom/?.len\\\"\", \"data_format\": \"{\\\"libraries\\\": [{\\\"input2\\\": null, \\\"__index__\\\": 0, \\\"input1\\\": null}], \\\"fastq_fasta\\\": \\\"fastq\\\", \\\"__current_case__\\\": 0}\", \"__page__\": 0}",
+ "tool_version": null,
+ "type": "tool",
+ "user_outputs": []
+ },
+ "6": {
+ "annotation": "",
+ "id": 6,
+ "input_connections": {
+ "space_consecutive_settings|filelist": {
+ "id": 5,
+ "output_name": "filelist"
+ },
+ "space_consecutive_settings|freq_cz": {
+ "id": 5,
+ "output_name": "cz"
+ },
+ "space_consecutive_settings|freq_cz_len": {
+ "id": 5,
+ "output_name": "cz_len"
+ }
+ },
+ "inputs": [],
+ "name": "Corrector AR",
+ "outputs": [
+ {
+ "name": "html_file",
+ "type": "html"
+ },
+ {
+ "name": "corrected_forward",
+ "type": "fa.gz"
+ },
+ {
+ "name": "corrected_reverse",
+ "type": "fa.gz"
+ },
+ {
+ "name": "corrected_single",
+ "type": "fa.gz"
+ }
+ ],
+ "position": {
+ "left": 450,
+ "top": 10
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "corrector_ar",
+ "tool_state": "{\"space_consecutive_settings\": \"{\\\"freq_cz_len\\\": null, \\\"__current_case__\\\": 0, \\\"ascii_shift_quality_value\\\": \\\"33\\\", \\\"consec_low_freq_cutoff\\\": \\\"3\\\", \\\"filelist\\\": null, \\\"space_consecutive_settings_type\\\": \\\"consecutive\\\", \\\"kmer_size\\\": \\\"17\\\", \\\"freq_cz\\\": null}\", \"default_full_settings\": \"{\\\"max_node_num\\\": \\\"15000000\\\", \\\"min_length_high_freq_region\\\": \\\"10\\\", \\\"min_length_trimmed_read\\\": \\\"50\\\", \\\"length_trim_low_qual_ends\\\": \\\"8\\\", \\\"trim_error_bases_Q\\\": \\\"0\\\", \\\"qual_threshold_error_bases\\\": \\\"30\\\", \\\"settings_type\\\": \\\"full\\\", \\\"convert_reads_into_paired_end_file\\\": \\\"1\\\", \\\"remove_suspicious_data\\\": \\\"0\\\", \\\"__current_case__\\\": 1, \\\"trim_suspicious_end_regions_Q\\\": \\\"1\\\", \\\"output_format\\\": \\\"1\\\", \\\"max_read_change\\\": \\\"2\\\"}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist-232ef8122d54/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null, \"__page__\": 0}",
+ "tool_version": null,
+ "type": "tool",
+ "user_outputs": []
+ },
+ "7": {
+ "annotation": "",
+ "id": 7,
+ "input_connections": {
+ "config_source|libraries_0|files_0|data_type|data_format|input1": {
+ "id": 6,
+ "output_name": "corrected_forward"
+ },
+ "config_source|libraries_0|files_0|data_type|data_format|input2": {
+ "id": 6,
+ "output_name": "corrected_reverse"
+ },
+ "config_source|libraries_1|files_0|data_type|data_format|input1": {
+ "id": 2,
+ "output_name": "output"
+ },
+ "config_source|libraries_1|files_0|data_type|data_format|input2": {
+ "id": 3,
+ "output_name": "output"
+ }
+ },
+ "inputs": [],
+ "name": "SOAPdenovo2",
+ "outputs": [
+ {
+ "name": "contig",
+ "type": "txt"
+ },
+ {
+ "name": "scafseq",
+ "type": "txt"
+ },
+ {
+ "name": "config",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 670,
+ "top": 10
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "soapdenovo2",
+ "tool_state": "{\"__page__\": 0, \"kmer_freq_cutoff\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist-232ef8122d54/tool-data/shared/ucsc/chrom/?.len\\\"\", \"default_full_settings\": \"{\\\"__current_case__\\\": 0, \\\"settings_type\\\": \\\"default\\\"}\", \"config_source\": \"{\\\"libraries\\\": [{\\\"files\\\": [{\\\"__index__\\\": 0, \\\"data_type\\\": {\\\"single_paired\\\": \\\"paired\\\", \\\"data_format\\\": {\\\"input2\\\": null, \\\"input1\\\": null, \\\"fastq_fasta\\\": \\\"fastq_gzipped\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 0}}], \\\"rd_len_cutoff\\\": \\\"\\\", \\\"avg_ins\\\": \\\"180\\\", \\\"rank\\\": \\\"1\\\", \\\"asm_flags\\\": \\\"3\\\", \\\"map_len\\\": \\\"\\\", \\\"pair_num_cutoff\\\": \\\"\\\", \\\"__index__\\\": 0, \\\"reverse_seq\\\": \\\"0\\\"}, {\\\"files\\\": [{\\\"__index__\\\": 0, \\\"data_type\\\": {\\\"single_paired\\\": \\\"paired\\\", \\\"data_format\\\": {\\\"input2\\\": null, \\\"input1\\\": null, \\\"fastq_fasta\\\": \\\"fastq\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0}}], \\\"rd_len_cutoff\\\": \\\"\\\", \\\"avg_ins\\\": \\\"3500\\\", \\\"rank\\\": \\\"2\\\", \\\"asm_flags\\\": \\\"2\\\", \\\"map_len\\\": \\\"31\\\", \\\"pair_num_cutoff\\\": \\\"11\\\", \\\"__index__\\\": 1, \\\"reverse_seq\\\": \\\"1\\\"}], \\\"max_read_length\\\": \\\"100\\\", \\\"config_source_select\\\": \\\"create\\\", \\\"__current_case__\\\": 1}\", \"kmer_size\": \"\\\"31\\\"\", \"resolve_repeats\": \"\\\"YES\\\"\", \"fill_gaps\": \"\\\"YES\\\"\", \"__rerun_remap_job_id__\": null}",
+ "tool_version": null,
+ "type": "tool",
+ "user_outputs": []
+ },
+ "8": {
+ "annotation": "",
+ "id": 8,
+ "input_connections": {
+ "config_source|own_file": {
+ "id": 7,
+ "output_name": "config"
+ },
+ "scaff_in": {
+ "id": 7,
+ "output_name": "scafseq"
+ }
+ },
+ "inputs": [],
+ "name": "GapCloser",
+ "outputs": [
+ {
+ "name": "scaff",
+ "type": "txt"
+ },
+ {
+ "name": "fill_info",
+ "type": "tabular"
+ }
+ ],
+ "position": {
+ "left": 890,
+ "top": 10
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "gapcloser",
+ "tool_state": "{\"__page__\": 0, \"scaff_in\": \"null\", \"default_full_settings\": \"{\\\"overlap_param\\\": \\\"31\\\", \\\"max_read_length\\\": \\\"70\\\", \\\"__current_case__\\\": 1, \\\"settings_type\\\": \\\"full\\\"}\", \"config_source\": \"{\\\"own_file\\\": null, \\\"config_source_select\\\": \\\"history\\\", \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist-232ef8122d54/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
+ "tool_version": null,
+ "type": "tool",
+ "user_outputs": []
+ },
+ "9": {
+ "annotation": "",
+ "id": 9,
+ "input_connections": {
+ "scafseq_gc_fa": {
+ "id": 8,
+ "output_name": "scaff"
+ }
+ },
+ "inputs": [],
+ "name": "Extract ACGT",
+ "outputs": [
+ {
+ "name": "scafseq_gc_ctg_fa",
+ "type": "txt"
+ }
+ ],
+ "position": {
+ "left": 1110,
+ "top": 10
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "extractACGT",
+ "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist-232ef8122d54/tool-data/shared/ucsc/chrom/?.len\\\"\", \"scafseq_gc_fa\": \"null\"}",
+ "tool_version": null,
+ "type": "tool",
+ "user_outputs": []
+ },
+ "10": {
+ "annotation": "",
+ "id": 10,
+ "input_connections": {
+ "contig_fasta": {
+ "id": 9,
+ "output_name": "scafseq_gc_ctg_fa"
+ },
+ "ref_fasta": {
+ "id": 4,
+ "output_name": "output"
+ },
+ "scaffold_fasta": {
+ "id": 8,
+ "output_name": "scaff"
+ }
+ },
+ "inputs": [],
+ "name": "GAGE evaluation",
+ "outputs": [
+ {
+ "name": "outfile",
+ "type": "Tabular"
+ }
+ ],
+ "position": {
+ "left": 1330,
+ "top": 10
+ },
+ "post_job_actions": {},
+ "tool_errors": null,
+ "tool_id": "get_correctness_stats",
+ "tool_state": "{\"__page__\": 0, \"ref_fasta\": \"null\", \"contig_fasta\": \"null\", \"scaffold_fasta\": \"null\", \"chromInfo\": \"\\\"/home/galaxy/galaxy-dist-232ef8122d54/tool-data/shared/ucsc/chrom/?.len\\\"\", \"__rerun_remap_job_id__\": null}",
+ "tool_version": null,
+ "type": "tool",
+ "user_outputs": []
+ }
+ }
+}
\ No newline at end of file
diff --git a/ro/make.sh b/ro/make.sh
new file mode 100755
index 0000000..f556909
--- /dev/null
+++ b/ro/make.sh
@@ -0,0 +1,96 @@
+#!/bin/bash
+#
+# RO manager script to test RO for features in Y2 review demo
+#
+
+source ../../ro.sh
+
+TESTRO="."
+RONAME="soapdenovo-v2"
+
+echo "--------"
+
+$RO config -v \
+ -b $ROPATH \
+ -r "http://sandbox.wf4ever-project.org/rodl/ROs/" \
+ -t "3c7483ac-e157-4cb3-97d5-8cf6e129f8e9" \
+ -n "Jun Zhao" \
+ -e "testuser@example.org"
+
+# ro config \
+# -b /Users/graham/Desktop/robase \
+# -r "http://sandbox.wf4ever-project.org/rodl/ROs/" \
+# -t "32801fc0-1df1-4e34-b" \
+# -n "Test user" \
+# -e "testuser@example.org"
+
+# -b /Users/graham/Desktop/robase \ # base directory for ROs
+# -r "http://sandbox.wf4ever-project.org/rodl/ROs/" \ # URI for ROSRS service used for ro push, checkout
+# -t "32801fc0-1df1-4e34-b" \ # Auth bearer token for ROSRS access
+# -n "Test user" \ # User name
+# -e "testuser@example.org" # User email
+
+# Remove old RO structure
+
+rm -rf .ro
+
+# show simple directory content
+
+ro create "RO for SOAPdenovo case study" -d . -i $RONAME
+
+# add all files from currenmt directory to RO
+
+ro add -a -d .
+
+# Show aggregated files
+
+ro list -d .
+
+# Basic information about the RO
+
+ro annotate . dcterms:descriptions "RO that aggregates the ISA documents, the nanopublication statements as well as information about the workflow used to produce the results."
+
+# Aggregate the ISAOWL and Nanopublication statements by links
+
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/isatab_distribution/1
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/isaowl_distribution/1
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/study/1
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/nanopubs
+
+
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/derived_data_file/3
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/raw_data_file/17
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/raw_data_file/18
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/raw_data_file/19
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/raw_data_file/20
+ro link . ore:aggregates http://w3id.org/isa/soapdenovo2/raw_data_file/21
+
+### Demonstrate of RO used for minimally preserving workflows
+
+# Add workflow description (wfdesc)
+
+# http://galaxy.cbiit.cuhk.edu.hk/u/gigascience/w/rluo2012-example-1-soapdenovo2-saureus
+
+ro annotate Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga -g Galaxy-wfdesc.rdf
+
+# Annotate selelcted input data
+
+ro link Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga roterms:inputSelected http://w3id.org/isa/soapdenovo2/raw_data_file/17
+ro link Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga roterms:inputSelected http://w3id.org/isa/soapdenovo2/raw_data_file/18
+ro link Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga roterms:inputSelected http://w3id.org/isa/soapdenovo2/raw_data_file/19
+ro link Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga roterms:inputSelected http://w3id.org/isa/soapdenovo2/raw_data_file/20
+ro link Workflows/Galaxy-Workflow-Workflow_constructed_from_history__reproduce_s.aureus_pipeline_.ga roterms:inputSelected http://w3id.org/isa/soapdenovo2/raw_data_file/21
+
+# Annotate output data
+ro annotate Outputs/gage.out.Tabular -g output.rdf
+
+# Show all annotations
+
+ro annotations
+
+# publish an RO
+
+ro push -d . -r "http://sandbox.wf4ever-project.org/rodl/ROs/" -t "73975122-9503-4000-ba52-d2c2d2bfccbb"
+
+# End.
+
diff --git a/ro/output.rdf b/ro/output.rdf
new file mode 100644
index 0000000..5e376ad
--- /dev/null
+++ b/ro/output.rdf
@@ -0,0 +1,60 @@
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+]>
+
+
+
+
+
+
+
+ Results calculating the N50 and corrected N50 scores
+ Results calculating the N50 and corrected N50 scores
+
+
+
+
+
+
+
+
+
+
+
+
+
+