Ray

tools/ray-json.json

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+{
+  "kmer_length": 23,
+  "input_files": [
+    {
+        "class": "File",
+         "path": "../../ray/S2_1.fastq"
+    },
+    {
+        "class": "File",
+        "path": "../../ray/S2_2.fastq"
+    }]
+}

tools/ray.cwl

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+#!/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."
+
+$namespaces:
+ edam: http://edamontology.org/
+ foaf: http://xmlns.com/foaf/0.1/
+ dct: http://purl.org/dc/terms/
+
+$schemas:
+ - http://edamontology.org/
+ - http://dublincore.org/2012/06/14/dcterms.rdf
+ - http://xmlns.com/foaf/spec/20140114.rdf
+
+inputs:
+ - id: kmer_length
+   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:
+     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: "RayOutput/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