{"tests": [{"data": {"status": "success", "inputs": {"reverse": {"src": "hda", "id": "5729865256bc2525"}, "min_overlap": "10", "outputs": ["assembled", "forward"], "cap": "0", "forward": {"src": "hda", "id": "2891970512fa2d5a"}, "min_assembly_length": "50"}, "job": {"inputs": {"forward": {"src": "hda", "id": "2891970512fa2d5a"}, "reverse": {"src": "hda", "id": "5729865256bc2525"}}, "update_time": "2015-02-11T12:50:31.576393", "tool_id": "iuc_pear", "outputs": {"unassembled_forward_reads": {"src": "hda", "id": "8155e4b4bf1581ff"}, "assembled_reads": {"src": "hda", "id": "54f2a3a23292eb07"}}, "stdout": " ____  _____    _    ____ \n|  _ \\| ____|  / \\  |  _ \\\n| |_) |  _|   / _ \\ | |_) |\n|  __/| |___ / ___ \\|  _ <\n|_|   |_____/_/   \\_\\_| \\_\\\n\nPEAR v0.9.6 [January 15, 2015]\n\nCitation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR\nZhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593\n\nForward reads file.................: /tmp/tmpSuVRNdfiles/000/dataset_1.dat\nReverse reads file.................: /tmp/tmpSuVRNdfiles/000/dataset_2.dat\nPHRED..............................: 33\nUsing empirical frequencies........: NO\nStatistical method.................: OES\nMaximum assembly length............: 999999\nMinimum assembly length............: 50\np-value............................: 0.010000\nQuality score threshold (trimming).: 0\nMinimum read size after trimming...: 1\nMaximal ratio of uncalled bases....: 1.000000\nMinimum overlap....................: 10\nScoring method.....................: Scaled score\nThreads............................: 1\n\nAllocating memory..................: 200,000,000 bytes\nAssemblying reads: 0%\rAssemblying reads: 100%\n\nAssembled reads ...................: 14 / 14 (100.000%)\nDiscarded reads ...................: 0 / 14 (0.000%)\nNot assembled reads ...............: 0 / 14 (0.000%)\nAssembled reads file...............: pear.assembled.fastq\nDiscarded reads file...............: pear.discarded.fastq\nUnassembled forward reads file.....: pear.unassembled.forward.fastq\nUnassembled reverse reads file.....: pear.unassembled.reverse.fastq\n", "command_line": "pear -f /tmp/tmpSuVRNdfiles/000/dataset_1.dat -r /tmp/tmpSuVRNdfiles/000/dataset_2.dat --output pear --p-value 0.01 --min-overlap 10 --min-asm-length 50 --min-trim-length 1 --quality-theshold 0 --max-uncalled-base 1.0 --test-method 1 --empirical-freqs -j \"${GALAXY_SLOTS:-8}\" --score-method 2 --cap 0", "exit_code": 0, "state": "ok", "create_time": "2015-02-11T12:50:27.868953", "params": {"max_uncalled_base": "\"1.0\"", "min_assembly_length": "\"50\"", "quality_threshold": "\"0\"", "empirical_freqs": "\"False\"", "nbase": "\"False\"", "outputs": "[\"assembled\", \"forward\"]", "cap": "\"0\"", "max_assembly_length": "\"0\"", "dbkey": "\"hg17\"", "min_overlap": "\"10\"", "score_method": "\"2\"", "test_method": "\"1\"", "min_trim_length": "\"1\"", "chromInfo": "\"/home/bag/projects/code/galaxy-central-1/tool-data/shared/ucsc/chrom/hg17.len\"", "pvalue": "\"0.01\""}, "stderr": "", "job_metrics": [], "model_class": "Job", "external_id": "6761", "id": "54f2a3a23292eb07", "user_email": "test@bx.psu.edu"}}, "id": "functional.test_toolbox.TestForTool_iuc_pear.test_tool_000000", "has_data": true}], "version": "0.1", "summary": {"num_skips": 0, "num_errors": 0, "num_failures": 0, "num_tests": 1}}