From 340aee9357f090e649eb7fd70bc3580b2218480f Mon Sep 17 00:00:00 2001
From: Ani <sharma.animesh@gmail.com>
Date: Thu, 17 Mar 2016 15:14:59 +0100
Subject: [PATCH 1/4] Create ray.cwl

---
 tools/ray.cwl | 75 +++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 75 insertions(+)
 create mode 100644 tools/ray.cwl

diff --git a/tools/ray.cwl b/tools/ray.cwl
new file mode 100644
index 000000000..b4d6a5c9f
--- /dev/null
+++ b/tools/ray.cwl
@@ -0,0 +1,75 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: cwl:draft-3 
+class: CommandLineTool
+description: "Ray is a parallel de novo genome assembler that utilises the message-passing interface everywhere and is implemented using peer-to-peer communication."
+
+$namespaces:
+ edam: http://edamontology.org/
+
+$schemas:
+ - http://edamontology.org/
+
+inputs:
+ - id: k-mer_size
+   type: int
+   description: "Selects the length of k-mers. The default value is 21."
+   label: "k-mer length"
+   - inputBinding: 
+     prefix: "-k"
+   
+ - id: input_files
+   label: "Paired end reads"
+   description: "Provides two files containing paired-end reads."
+    - type: array
+      items: File
+      format: edam:format_1930
+      - inputBinding:
+        prefix: "-p"
+   
+outputs:
+ - id: contigs
+   type: File
+   description: "Contiguous sequences in FASTA format"
+   format: edam:format_1929
+   outputBinding:
+    glob: "Contigs.fasta"
+  
+baseCommand: "Ray"
+
+dct:creator:
+- class: foaf:Organization
+  foaf:name: "Norwegian University of Science and Technology"
+  foaf:member:
+  - class: foaf:Person
+    foaf:mbox: "mailto:animesh.sharma@ntnu.no"
+    foaf:name: "Animesh Sharma"
+    
+#/Ray -o testtt -p S2_1.fastq S2_2.fastq -k 31
+#ContigLengths.txt
+#Contigs.fasta
+#Contigs.fasta.kmer.dna.output.default
+#Contigs.fasta.kmer.dna.output.default.func.txt
+#Contigs.fasta.kmer.dna.output.default.otu.txt
+#CoverageDistributionAnalysis.txt
+#CoverageDistribution.txt
+#degreeDistribution.txt
+#ElapsedTime.txt
+#FilePartition.txt
+#GraphPartition.txt
+#LibraryData.xml
+#LibraryStatistics.txt
+#NeighbourhoodRelations.txt
+#NetworkTest.txt
+#NumberOfSequences.txt
+#OutputNumbers.txt
+#ParallelPaths.txt
+#RayCommand.txt
+#RayPlatform_Version.txt
+#RaySmartCommand.txt
+#RayVersion.txt
+#ScaffoldComponents.txt
+#ScaffoldLengths.txt
+#ScaffoldLinks.txt
+#Scaffolds.fasta
+#SeedLengthDistribution.txt
+#SequencePartition.txt

From 08e573e87368df34e3eef10b8bce071f20245711 Mon Sep 17 00:00:00 2001
From: Animesh Sharma <sharma.animesh@gmail.com>
Date: Thu, 17 Mar 2016 15:40:33 +0100
Subject: [PATCH 2/4] IT works!

---
 tools/ray.cwl | 19 ++++++++++++-------
 1 file changed, 12 insertions(+), 7 deletions(-)

diff --git a/tools/ray.cwl b/tools/ray.cwl
index b4d6a5c9f..822efae2a 100644
--- a/tools/ray.cwl
+++ b/tools/ray.cwl
@@ -5,26 +5,31 @@ description: "Ray is a parallel de novo genome assembler that utilises the messa
 
 $namespaces:
  edam: http://edamontology.org/
+ foaf: http://xmlns.com/foaf/0.1/
+ dct: http://purl.org/dc/terms/
 
 $schemas:
  - http://edamontology.org/
+ - http://dublincore.org/2012/06/14/dcterms.rdf
+ - http://xmlns.com/foaf/spec/20140114.rdf
 
 inputs:
- - id: k-mer_size
+ - id: kmer_length
    type: int
    description: "Selects the length of k-mers. The default value is 21."
    label: "k-mer length"
-   - inputBinding: 
+   inputBinding:
      prefix: "-k"
    
  - id: input_files
    label: "Paired end reads"
    description: "Provides two files containing paired-end reads."
-    - type: array
-      items: File
-      format: edam:format_1930
-      - inputBinding:
-        prefix: "-p"
+   type:
+     type: array
+     items: File
+     format: edam:format_1930
+     inputBinding:
+       prefix: "-p"
    
 outputs:
  - id: contigs

From b722ac8e3b561ad3925350c8b6c531bf1c9c3144 Mon Sep 17 00:00:00 2001
From: Animesh Sharma <sharma.animesh@gmail.com>
Date: Thu, 17 Mar 2016 15:48:34 +0100
Subject: [PATCH 3/4] fixed output name

---
 tools/ray.cwl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tools/ray.cwl b/tools/ray.cwl
index 822efae2a..15a3e63b0 100644
--- a/tools/ray.cwl
+++ b/tools/ray.cwl
@@ -37,7 +37,7 @@ outputs:
    description: "Contiguous sequences in FASTA format"
    format: edam:format_1929
    outputBinding:
-    glob: "Contigs.fasta"
+    glob: "RayOutput/Contigs.fasta"
   
 baseCommand: "Ray"
 

From 5e9be73dfe93edb9335cb1b103b6f8e97e65c650 Mon Sep 17 00:00:00 2001
From: Animesh Sharma <sharma.animesh@gmail.com>
Date: Thu, 17 Mar 2016 16:27:39 +0100
Subject: [PATCH 4/4] fix input bindings

---
 tools/ray-json.json | 12 ++++++++++++
 tools/ray.cwl       |  4 ++--
 2 files changed, 14 insertions(+), 2 deletions(-)
 create mode 100644 tools/ray-json.json

diff --git a/tools/ray-json.json b/tools/ray-json.json
new file mode 100644
index 000000000..37e0a9a15
--- /dev/null
+++ b/tools/ray-json.json
@@ -0,0 +1,12 @@
+{
+  "kmer_length": 23,
+  "input_files": [
+    {
+        "class": "File",
+         "path": "../../ray/S2_1.fastq"
+    },
+    {
+        "class": "File",
+        "path": "../../ray/S2_2.fastq"
+    }]
+}
diff --git a/tools/ray.cwl b/tools/ray.cwl
index 15a3e63b0..924db5b55 100644
--- a/tools/ray.cwl
+++ b/tools/ray.cwl
@@ -28,8 +28,8 @@ inputs:
      type: array
      items: File
      format: edam:format_1930
-     inputBinding:
-       prefix: "-p"
+   inputBinding:
+     prefix: "-p"
    
 outputs:
  - id: contigs