created a test data set: FNA, FAA, GFF from IMP3 test data, readme and set-up...

created a test data set: FNA, FAA, GFF from IMP3 test data, readme and set-up script, test config (issue #30)

test/README.md

+Input files
+
+```bash
+# *.fna, *.faa and *.gff
+rsync -avP /work/projects/ecosystem_biology/local_tools/IMP3/test/testRAW/run150320/Analysis/annotation/prokka.gff test_sample.gff
+rsync -avP /work/projects/ecosystem_biology/local_tools/IMP3/test/testRAW/run150320/Analysis/annotation/prokka.fna test_sample.fna
+rsync -avP /work/projects/ecosystem_biology/local_tools/IMP3/test/testRAW/run150320/Analysis/annotation/prokka.faa test_sample.faa
+
+# set-up: modify files, create other required files
+./set-up.sh
+```

test/set-up.sh

+#!/bin/bash -l
+
+# modify *.faa: rm record descriptions
+sed -i '/^>/ s/ .*//' test_sample.faa
+
+# *.gff to *.contig: contig ID, feature ID
+grep -v '^#' test_sample.gff | cut -f1,9 | cut -d';' -f1 | sed 's/ID=//' > test_sample.contig

test/test_config.yaml

+# List of sample names, i.e. base names of input files
+# Each sample should have 3 files: *.fna, *.faa, *.contig
+input_file: ["test_sample"]
+
+# Unique project name (used in output directory name)
+project: "output_test"
+
+# Data path
+# Output will be saved in <OUTDIR>/<project>
+OUTDIR: "test"
+
+# Split size of FASTA files (default: 10 000 seqs/file)
+size_fasta: 100000
+
+# Workflow (default: "complete")
+# complete: complete pipeline: toxin + virulence + (AMR + MGE) prediction
+# Tox:      toxin prediction
+# Vir:      virulence prediction
+# AMR:      antimicrobial resistance (AMR) & mobile genetic element (MGE) prediction
+workflow: "complete"
+
+###########
+# SignalP #
+###########
+# SignalP
+signalp: "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/SignalP/signalp-4.1/signalp"
+
+#########
+# Toxin #
+#########
+# HMM
+hmmscan_tool: "hmmsearch"
+hmm_file: "databases/toxins/combined_Toxin.hmm"
+
+#############
+# Virulence #
+#############
+# HMM
+vir_hmm_file: "databases/virulence/Virulence_factor.hmm"
+
+#######
+# AMR #
+#######
+# DeepARG
+deep_ARG: "submodules/deeparg-ss/deepARG.py"
+
+# Plasflow
+Plasflow: "PlasFlow.py"
+
+# Virsorter
+virsorter: "wrapper_phage_contigs_sorter_iPlant.pl"
+virsorter_data: "scripts/virsorter-data"
+
+# VirFinder
+DeepVirFinder: "submodules/DeepVirFinder/dvf.py"