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Changeset 1:d20e391eb22f (2015-12-22)

Previous changeset 0:e416c7c26977 (2015-12-21) Next changeset 2:f2537346a7b7 (2016-02-18)

Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260

added:
all_fasta.loc.sample
fimo_wrapper.py
test-data/fimo_output_almost-gff_1.txt
test-data/fimo_output_almost-gff_2.txt
test-data/fimo_output_html_1.html
test-data/fimo_output_html_2.html
test-data/fimo_output_interval_1.txt
test-data/fimo_output_interval_2.txt
test-data/fimo_output_txt_1.txt
test-data/fimo_output_txt_2.txt
test-data/fimo_output_xml_1.xml
test-data/fimo_output_xml_2.xml
test-data/phiX.fasta
tool_data_table_conf.xml.sample

diff -r e416c7c26977 -r d20e391eb22f all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/all_fasta.loc.sample Tue Dec 22 17:02:11 2015 -0500

@@ -0,0 +1,18 @@
+#This file lists the locations and dbkeys of all the fasta files
+#under the "genome" directory (a directory that contains a directory
+#for each build). The script extract_fasta.py will generate the file
+#all_fasta.loc. This file has the format (white space characters are
+#TAB characters):
+#
+#<unique_build_id> <dbkey> <display_name> <file_path>
+#
+#So, all_fasta.loc could look something like this:
+#
+#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
+#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
+#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
+#
+#Your all_fasta.loc file should contain an entry for each individual
+#fasta file. So there will be multiple fasta files for each build,
+#such as with hg19 above.
+#

diff -r e416c7c26977 -r d20e391eb22f fimo_wrapper.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/fimo_wrapper.py Tue Dec 22 17:02:11 2015 -0500

[

@@ -0,0 +1,134 @@
+#!/usr/bin/env python
+import argparse
+import os
+import shutil
+import string
+import subprocess
+import sys
+import tempfile
+
+BUFFSIZE = 1048576
+# Translation table for reverse Complement, with ambiguity codes.
+DNA_COMPLEMENT = string.maketrans("ACGTRYKMBDHVacgtrykmbdhv", "TGCAYRMKVHDBtgcayrmkvhdb")
+
+
+def reverse(sequence):
+    # Reverse sequence string.
+    return sequence[::-1]
+
+
+def dna_complement(sequence):
+    # Complement DNA sequence string.
+    return sequence.translate(DNA_COMPLEMENT)
+
+
+def dna_reverse_complement(sequence):
+    # Returns the reverse complement of the sequence.
+    sequence = reverse(sequence)
+    return dna_complement(sequence)
+
+
+def stop_err(msg):
+    sys.stderr.write(msg)
+    sys.exit(1)
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--input_motifs', dest='input_motifs', help='MEME output formatted files for input to fimo')
+parser.add_argument('--input_fasta', dest='input_fasta', help='Fassta sequence file')
+parser.add_argument('--options_type', dest='options_type', help='Basic or Advance options')
+parser.add_argument('--input_psp', dest='input_psp', default=None, help='File containing position specific priors')
+parser.add_argument('--input_prior_dist', dest='input_prior_dist', default=None, help='File containing binned distribution of priors')
+parser.add_argument('--alpha', dest='alpha', type=float, default=1.0, help='The alpha parameter for calculating position specific priors')
+parser.add_argument('--bgfile', dest='bgfile', default=None, help='Background file type, used only if not "default"')
+parser.add_argument('--max_strand', action='store_true', help='If matches on both strands at a given position satisfy the output threshold, only report the match for the strand with the higher score')
+parser.add_argument('--max_stored_scores', dest='max_stored_scores', type=int, help='Maximum score count to store')
+parser.add_argument('--motif', dest='motifs', action='append', default=[], help='Specify motif by id')
+parser.add_argument('--motif_pseudo', dest='motif_pseudo', type=float, default=0.1, help='Pseudocount to add to counts in motif matrix')
+parser.add_argument('--no_qvalue', action='store_true', help='Do not compute a q-value for each p-value')
+parser.add_argument('--norc', action='store_true', help='Do not score the reverse complement DNA strand')
+parser.add_argument('--output_path', dest='output_path', help='Output files directory')
+parser.add_argument('--parse_genomic_coord', action='store_true', help='Check each sequence header for UCSC style genomic coordinates')
+parser.add_argument('--qv_thresh', action='store_true', help='Use q-values for the output threshold')
+parser.add_argument('--thresh', dest='thresh', type=float, help='p-value threshold')
+parser.add_argument('--gff_output', dest='gff_output', help='Gff output file')
+parser.add_argument('--html_output', dest='html_output', help='HTML output file')
+parser.add_argument('--interval_output', dest='interval_output', help='Interval output file')
+parser.add_argument('--txt_output', dest='txt_output', help='Text output file')
+parser.add_argument('--xml_output', dest='xml_output', help='XML output file')
+args = parser.parse_args()
+
+fimo_cmd_list = ['fimo']
+if args.options_type == 'advanced':
+    fimo_cmd_list.append('--alpha %4f' % args.alpha)
+    if args.bgfile is not None:
+        fimo_cmd_list.append('--bgfile "%s"' % args.bgfile)
+    if args.max_strand:
+        fimo_cmd_list.append('--max-strand')
+    fimo_cmd_list.append('--max-stored-scores %d' % args.max_stored_scores)
+    if len(args.motifs) > 0:
+        for motif in args.motifs:
+            fimo_cmd_list.append('--motif "%s"' % motif)
+    fimo_cmd_list.append('--motif-pseudo %4f' % args.motif_pseudo)
+    if args.no_qvalue:
+        fimo_cmd_list.append('--no-qvalue')
+    if args.norc:
+        fimo_cmd_list.append('--norc')
+    if args.parse_genomic_coord:
+        fimo_cmd_list.append('--parse-genomic-coord')
+    if args.qv_thresh:
+        fimo_cmd_list.append('--qv-thresh')
+    fimo_cmd_list.append('--thresh %4f' % args.thresh)
+    if args.input_psp is not None:
+        fimo_cmd_list.append('--psp "%s"' % args.input_psp)
+    if args.input_prior_dist is not None:
+        fimo_cmd_list.append('--prior-dist "%s"' % args.input_prior_dist)
+fimo_cmd_list.append('--o "%s"' % (args.output_path))
+fimo_cmd_list.append('--verbosity 1')
+fimo_cmd_list.append(args.input_motifs)
+fimo_cmd_list.append(args.input_fasta)
+
+fimo_cmd = ' '.join(fimo_cmd_list)
+
+try:
+    tmp_stderr = tempfile.NamedTemporaryFile()
+    proc = subprocess.Popen(args=fimo_cmd, shell=True, stderr=tmp_stderr)
+    returncode = proc.wait()
+    tmp_stderr.seek(0)
+    stderr = ''
+    try:
+        while True:
+            stderr += tmp_stderr.read(BUFFSIZE)
+            if not stderr or len(stderr) % BUFFSIZE != 0:
+                break
+    except OverflowError:
+        pass
+    if returncode != 0:
+        stop_err(stderr)
+except Exception, e:
+    stop_err('Error running FIMO:\n%s' % str(e))
+
+shutil.move(os.path.join(args.output_path, 'fimo.txt'), args.txt_output)
+shutil.move(os.path.join(args.output_path, 'fimo.gff'), args.gff_output)
+shutil.move(os.path.join(args.output_path, 'fimo.xml'), args.xml_output)
+shutil.move(os.path.join(args.output_path, 'fimo.html'), args.html_output)
+
+out_file = open(args.interval_output, 'wb')
+out_file.write("#%s\n" % "\t".join(("chr", "start", "end", "pattern name", "score", "strand", "matched sequence", "p-value", "q-value")))
+for line in open(args.txt_output):
+    if line.startswith('#'):
+        continue
+    fields = line.rstrip("\n\r").split("\t")
+    start, end = int(fields[2]), int(fields[3])
+    sequence = fields[7]
+    if start > end:
+        # Flip start and end and set strand.
+        start, end = end, start
+        strand = "-"
+        # We want sequences relative to strand; FIMO always provides + stranded sequence.
+        sequence = dna_reverse_complement(sequence)
+    else:
+        strand = "+"
+    # Make 0-based start position.
+    start -= 1
+    out_file.write("%s\n" % "\t".join([fields[1], str(start), str(end), fields[0], fields[4], strand, sequence, fields[5], fields[6]]))
+out_file.close()

diff -r e416c7c26977 -r d20e391eb22f test-data/fimo_output_almost-gff_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_almost-gff_1.txt Tue Dec 22 17:02:11 2015 -0500

b'@@ -0,0 +1,100 @@\n+##gff-version 3\n+phiX174\tfimo\tpolypeptide_motif\t1388\t1398\t102\t+\t.\tName=1;ID=1-1-phiX174;pvalue=6.36e-11;qvalue= 1.25e-09;sequence=AATATCTATAA;\n+phiX174\tfimo\tpolypeptide_motif\t847\t857\t102\t+\t.\tName=1;ID=1-2-phiX174;pvalue=7.02e-11;qvalue= 1.25e-09;sequence=AATGTCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t2301\t2311\t99.6\t+\t.\tName=1;ID=1-3-phiX174;pvalue=1.08e-10;qvalue= 1.29e-09;sequence=AGGTTATAACG;\n+phiX174\tfimo\tpolypeptide_motif\t5063\t5073\t95.6\t+\t.\tName=1;ID=1-4-phiX174;pvalue=2.73e-10;qvalue= 2.25e-09;sequence=AGGAGCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t989\t999\t 95\t+\t.\tName=1;ID=1-5-phiX174;pvalue=3.15e-10;qvalue= 2.25e-09;sequence=TGAGGATAAAT;\n+phiX174\tfimo\tpolypeptide_motif\t4713\t4723\t91.1\t+\t.\tName=1;ID=1-6-phiX174;pvalue=7.74e-10;qvalue= 3.48e-09;sequence=GACTGCTATCA;\n+phiX174\tfimo\tpolypeptide_motif\t5048\t5058\t90.7\t+\t.\tName=1;ID=1-7-phiX174;pvalue=8.51e-10;qvalue= 3.48e-09;sequence=TGCTGCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t855\t865\t90.6\t+\t.\tName=1;ID=1-8-phiX174;pvalue=8.64e-10;qvalue= 3.48e-09;sequence=AAGGTAAAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t3155\t3165\t90.1\t+\t.\tName=1;ID=1-9-phiX174;pvalue=9.76e-10;qvalue= 3.48e-09;sequence=TATGGCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t5009\t5019\t90.1\t+\t.\tName=1;ID=1-10-phiX174;pvalue=9.76e-10;qvalue= 3.48e-09;sequence=TGTGGCTAAAT;\n+phiX174\tfimo\tpolypeptide_motif\t814\t824\t88.9\t+\t.\tName=1;ID=1-11-phiX174;pvalue=1.28e-09;qvalue= 4.14e-09;sequence=TGCGTCAAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t2832\t2842\t88.5\t+\t.\tName=1;ID=1-12-phiX174;pvalue=1.42e-09;qvalue= 4.23e-09;sequence=TTGGTCTAACT;\n+phiX174\tfimo\tpolypeptide_motif\t3830\t3840\t87.7\t+\t.\tName=1;ID=1-13-phiX174;pvalue=1.7e-09;qvalue= 4.68e-09;sequence=TATTGATAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t3560\t3570\t87.2\t+\t.\tName=1;ID=1-14-phiX174;pvalue=1.89e-09;qvalue= 4.82e-09;sequence=TGCGTCTATTA;\n+phiX174\tfimo\tpolypeptide_motif\t2882\t2892\t86.4\t+\t.\tName=1;ID=1-15-phiX174;pvalue=2.29e-09;qvalue= 5.46e-09;sequence=AGGTTATTAAA;\n+phiX174\tfimo\tpolypeptide_motif\t4453\t4463\t85.9\t+\t.\tName=1;ID=1-16-phiX174;pvalue=2.58e-09;qvalue= 5.75e-09;sequence=AAGGTATTAAG;\n+phiX174\tfimo\tpolypeptide_motif\t2493\t2503\t85.1\t+\t.\tName=1;ID=1-17-phiX174;pvalue=3.06e-09;qvalue= 5.79e-09;sequence=GACACCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t4104\t4114\t85.1\t+\t.\tName=1;ID=1-18-phiX174;pvalue=3.08e-09;qvalue= 5.79e-09;sequence=GGCTTCCATAA;\n+phiX174\tfimo\tpolypeptide_motif\t4955\t4965\t85.1\t+\t.\tName=1;ID=1-19-phiX174;pvalue=3.08e-09;qvalue= 5.79e-09;sequence=TGATGCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t1885\t1895\t84.4\t+\t.\tName=1;ID=1-20-phiX174;pvalue=3.61e-09;qvalue= 6.45e-09;sequence=TGCGACTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t3376\t3386\t84.2\t+\t.\tName=1;ID=1-21-phiX174;pvalue=3.81e-09;qvalue= 6.48e-09;sequence=AGAATCAAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t52\t62\t83.9\t+\t.\tName=1;ID=1-22-phiX174;pvalue=4.06e-09;qvalue= 6.58e-09;sequence=TGAGTCGAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t1390\t1400\t83.7\t+\t.\tName=1;ID=1-23-phiX174;pvalue=4.26e-09;qvalue= 6.61e-09;sequence=TATCTATAACA;\n+phiX174\tfimo\tpolypeptide_motif\t2017\t2027\t83.4\t+\t.\tName=1;ID=1-24-phiX174;pvalue=4.6e-09;qvalue= 6.85e-09;sequence=TTCGTCTAAGA;\n+phiX174\tfimo\tpolypeptide_motif\t1000\t1010\t83.1\t+\t.\tName=1;ID=1-25-phiX174;pvalue=4.88e-09;qvalue= 6.97e-09;sequence=TATGTCTAATA;\n+phiX174\tfimo\tpolypeptide_motif\t1555\t1565\t82.5\t+\t.\tName=1;ID=1-26-phiX174;pvalue=5.58e-09;qvalue= 7.37e-09;sequence=GACTTCTACCA;\n+phiX174\tfimo\tpolypeptide_motif\t4430\t4440\t82.5\t+\t.\tName=1;ID=1-27-phiX174;pvalue=5.62e-09;qvalue= 7.37e-09;sequence=TGAGTATAATT;\n+phiX174\tfimo\tpolypeptide_motif\t1927\t1937\t82.3\t+\t.\tName=1;ID=1-28-phiX174;pvalue=5.82e-09;qvalue= 7.37e-09;sequence=GACTTATACCG;\n+phiX174\tfimo\tpolypeptide_motif\t2981\t2991\t82.1\t+\t.\tName=1;ID=1-29-phiX174;pvalue=6.13e-09;qvalue= 7.37e-09;sequence=CATGTCTAAAT;\n+phiX174\tfimo\tpolypeptide_motif\t4203\t4213\t 82\t+\t.\tName=1;ID=1-30-phiX174;pvalue=6.34e-09;qvalue= 7.37e-09;sequence=GACGGCCATAA;\n+phiX174\tfimo\tpolypeptide_motif\t1669\t1679\t81.9\t+\t.\tName=1;ID=1-31-phiX174;pvalue=6.4e-09;qvalue= 7.37e-09;sequence=TGGAGG'..b'= 1.31e-08;sequence=AAATGAGAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t1491\t1501\t75.9\t+\t.\tName=1;ID=1-69-phiX174;pvalue=2.55e-08;qvalue= 1.32e-08;sequence=GCCATCTCAAA;\n+phiX174\tfimo\tpolypeptide_motif\t434\t444\t75.7\t+\t.\tName=1;ID=1-70-phiX174;pvalue=2.67e-08;qvalue= 1.36e-08;sequence=GGCCTCTATTA;\n+phiX174\tfimo\tpolypeptide_motif\t4565\t4575\t75.6\t+\t.\tName=1;ID=1-71-phiX174;pvalue=2.73e-08;qvalue= 1.36e-08;sequence=TTGGTTTATCG;\n+phiX174\tfimo\tpolypeptide_motif\t102\t112\t75.6\t+\t.\tName=1;ID=1-72-phiX174;pvalue=2.75e-08;qvalue= 1.36e-08;sequence=GAATTAAATCG;\n+phiX174\tfimo\tpolypeptide_motif\t903\t913\t75.5\t+\t.\tName=1;ID=1-73-phiX174;pvalue=2.82e-08;qvalue= 1.38e-08;sequence=GAGGTACTAAA;\n+phiX174\tfimo\tpolypeptide_motif\t4748\t4758\t75.2\t+\t.\tName=1;ID=1-74-phiX174;pvalue=3.01e-08;qvalue= 1.45e-08;sequence=TACAGCTAATG;\n+phiX174\tfimo\tpolypeptide_motif\t2622\t2632\t 75\t+\t.\tName=1;ID=1-75-phiX174;pvalue=3.16e-08;qvalue= 1.5e-08;sequence=TGCTGATATTG;\n+phiX174\tfimo\tpolypeptide_motif\t467\t477\t74.7\t+\t.\tName=1;ID=1-76-phiX174;pvalue=3.35e-08;qvalue= 1.57e-08;sequence=TTTGGATTTAA;\n+phiX174\tfimo\tpolypeptide_motif\t4033\t4043\t74.6\t+\t.\tName=1;ID=1-77-phiX174;pvalue=3.44e-08;qvalue= 1.58e-08;sequence=AGCGTATCGAG;\n+phiX174\tfimo\tpolypeptide_motif\t1348\t1358\t74.6\t+\t.\tName=1;ID=1-78-phiX174;pvalue=3.46e-08;qvalue= 1.58e-08;sequence=TACCAATAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t239\t249\t74.4\t+\t.\tName=1;ID=1-79-phiX174;pvalue=3.62e-08;qvalue= 1.64e-08;sequence=AGTGGCTTAAT;\n+phiX174\tfimo\tpolypeptide_motif\t500\t510\t74.1\t+\t.\tName=1;ID=1-80-phiX174;pvalue=3.84e-08;qvalue= 1.71e-08;sequence=GACGAGTAACA;\n+phiX174\tfimo\tpolypeptide_motif\t3001\t3011\t 74\t+\t.\tName=1;ID=1-81-phiX174;pvalue=3.93e-08;qvalue= 1.73e-08;sequence=GCGGTCAAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t3776\t3786\t 74\t+\t.\tName=1;ID=1-82-phiX174;pvalue=3.98e-08;qvalue= 1.73e-08;sequence=TATTTCTAATG;\n+phiX174\tfimo\tpolypeptide_motif\t2026\t2036\t73.9\t+\t.\tName=1;ID=1-83-phiX174;pvalue=4.06e-08;qvalue= 1.75e-08;sequence=GAAGTTTAAGA;\n+phiX174\tfimo\tpolypeptide_motif\t4237\t4247\t73.8\t+\t.\tName=1;ID=1-84-phiX174;pvalue=4.12e-08;qvalue= 1.75e-08;sequence=AGTTTGTATCT;\n+phiX174\tfimo\tpolypeptide_motif\t803\t813\t73.7\t+\t.\tName=1;ID=1-85-phiX174;pvalue=4.24e-08;qvalue= 1.78e-08;sequence=AGAAGAAAACG;\n+phiX174\tfimo\tpolypeptide_motif\t3770\t3780\t73.6\t+\t.\tName=1;ID=1-86-phiX174;pvalue=4.35e-08;qvalue= 1.81e-08;sequence=AAAGGATATTT;\n+phiX174\tfimo\tpolypeptide_motif\t3429\t3439\t73.5\t+\t.\tName=1;ID=1-87-phiX174;pvalue=4.45e-08;qvalue= 1.82e-08;sequence=GAGATGCAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t99\t109\t73.5\t+\t.\tName=1;ID=1-88-phiX174;pvalue=4.48e-08;qvalue= 1.82e-08;sequence=TACGAATTAAA;\n+phiX174\tfimo\tpolypeptide_motif\t67\t77\t73.2\t+\t.\tName=1;ID=1-89-phiX174;pvalue=4.78e-08;qvalue= 1.92e-08;sequence=TCTTGATAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t5332\t5342\t72.9\t+\t.\tName=1;ID=1-90-phiX174;pvalue=5.13e-08;qvalue= 2.01e-08;sequence=ATCTGCTCAAA;\n+phiX174\tfimo\tpolypeptide_motif\t277\t287\t72.9\t+\t.\tName=1;ID=1-91-phiX174;pvalue=5.14e-08;qvalue= 2.01e-08;sequence=TTTAGATATGA;\n+phiX174\tfimo\tpolypeptide_motif\t4338\t4348\t72.8\t+\t.\tName=1;ID=1-92-phiX174;pvalue=5.18e-08;qvalue= 2.01e-08;sequence=GGGGACGAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t3812\t3822\t72.8\t+\t.\tName=1;ID=1-93-phiX174;pvalue=5.28e-08;qvalue= 2.03e-08;sequence=GGTTGATATTT;\n+phiX174\tfimo\tpolypeptide_motif\t1909\t1919\t72.6\t+\t.\tName=1;ID=1-94-phiX174;pvalue=5.51e-08;qvalue= 2.08e-08;sequence=TAACGCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t3000\t3010\t72.6\t+\t.\tName=1;ID=1-95-phiX174;pvalue=5.54e-08;qvalue= 2.08e-08;sequence=GGCGGTCAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t3891\t3901\t72.4\t+\t.\tName=1;ID=1-96-phiX174;pvalue=5.75e-08;qvalue= 2.11e-08;sequence=ATTGGCTCTAA;\n+phiX174\tfimo\tpolypeptide_motif\t3079\t3089\t72.4\t+\t.\tName=1;ID=1-97-phiX174;pvalue=5.76e-08;qvalue= 2.11e-08;sequence=CTGGTATTAAA;\n+phiX174\tfimo\tpolypeptide_motif\t37\t47\t72.4\t+\t.\tName=1;ID=1-98-phiX174;pvalue=5.79e-08;qvalue= 2.11e-08;sequence=TTCGGATATTT;\n+phiX174\tfimo\tpolypeptide_motif\t380\t390\t72.2\t+\t.\tName=1;ID=1-99-phiX174;pvalue=6.01e-08;qvalue= 2.17e-08;sequence=GTAAGAAATCA;\n'

diff -r e416c7c26977 -r d20e391eb22f test-data/fimo_output_almost-gff_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_almost-gff_2.txt Tue Dec 22 17:02:11 2015 -0500

b'@@ -0,0 +1,100 @@\n+##gff-version 3\n+phiX174\tfimo\tpolypeptide_motif\t1388\t1398\t102\t+\t.\tName=1;ID=1-1-phiX174;pvalue=6.36e-11;sequence=AATATCTATAA;\n+phiX174\tfimo\tpolypeptide_motif\t847\t857\t102\t+\t.\tName=1;ID=1-2-phiX174;pvalue=7.02e-11;sequence=AATGTCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t2301\t2311\t99.6\t+\t.\tName=1;ID=1-3-phiX174;pvalue=1.08e-10;sequence=AGGTTATAACG;\n+phiX174\tfimo\tpolypeptide_motif\t5063\t5073\t95.6\t+\t.\tName=1;ID=1-4-phiX174;pvalue=2.73e-10;sequence=AGGAGCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t989\t999\t 95\t+\t.\tName=1;ID=1-5-phiX174;pvalue=3.15e-10;sequence=TGAGGATAAAT;\n+phiX174\tfimo\tpolypeptide_motif\t4713\t4723\t91.1\t+\t.\tName=1;ID=1-6-phiX174;pvalue=7.74e-10;sequence=GACTGCTATCA;\n+phiX174\tfimo\tpolypeptide_motif\t5048\t5058\t90.7\t+\t.\tName=1;ID=1-7-phiX174;pvalue=8.51e-10;sequence=TGCTGCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t855\t865\t90.6\t+\t.\tName=1;ID=1-8-phiX174;pvalue=8.64e-10;sequence=AAGGTAAAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t3155\t3165\t90.1\t+\t.\tName=1;ID=1-9-phiX174;pvalue=9.76e-10;sequence=TATGGCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t5009\t5019\t90.1\t+\t.\tName=1;ID=1-10-phiX174;pvalue=9.76e-10;sequence=TGTGGCTAAAT;\n+phiX174\tfimo\tpolypeptide_motif\t814\t824\t88.9\t+\t.\tName=1;ID=1-11-phiX174;pvalue=1.28e-09;sequence=TGCGTCAAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t2832\t2842\t88.5\t+\t.\tName=1;ID=1-12-phiX174;pvalue=1.42e-09;sequence=TTGGTCTAACT;\n+phiX174\tfimo\tpolypeptide_motif\t3830\t3840\t87.7\t+\t.\tName=1;ID=1-13-phiX174;pvalue=1.7e-09;sequence=TATTGATAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t3560\t3570\t87.2\t+\t.\tName=1;ID=1-14-phiX174;pvalue=1.89e-09;sequence=TGCGTCTATTA;\n+phiX174\tfimo\tpolypeptide_motif\t2882\t2892\t86.4\t+\t.\tName=1;ID=1-15-phiX174;pvalue=2.29e-09;sequence=AGGTTATTAAA;\n+phiX174\tfimo\tpolypeptide_motif\t4453\t4463\t85.9\t+\t.\tName=1;ID=1-16-phiX174;pvalue=2.58e-09;sequence=AAGGTATTAAG;\n+phiX174\tfimo\tpolypeptide_motif\t2493\t2503\t85.1\t+\t.\tName=1;ID=1-17-phiX174;pvalue=3.06e-09;sequence=GACACCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t4104\t4114\t85.1\t+\t.\tName=1;ID=1-18-phiX174;pvalue=3.08e-09;sequence=GGCTTCCATAA;\n+phiX174\tfimo\tpolypeptide_motif\t4955\t4965\t85.1\t+\t.\tName=1;ID=1-19-phiX174;pvalue=3.08e-09;sequence=TGATGCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t1885\t1895\t84.4\t+\t.\tName=1;ID=1-20-phiX174;pvalue=3.61e-09;sequence=TGCGACTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t3376\t3386\t84.2\t+\t.\tName=1;ID=1-21-phiX174;pvalue=3.81e-09;sequence=AGAATCAAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t52\t62\t83.9\t+\t.\tName=1;ID=1-22-phiX174;pvalue=4.06e-09;sequence=TGAGTCGAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t1390\t1400\t83.7\t+\t.\tName=1;ID=1-23-phiX174;pvalue=4.26e-09;sequence=TATCTATAACA;\n+phiX174\tfimo\tpolypeptide_motif\t2017\t2027\t83.4\t+\t.\tName=1;ID=1-24-phiX174;pvalue=4.6e-09;sequence=TTCGTCTAAGA;\n+phiX174\tfimo\tpolypeptide_motif\t1000\t1010\t83.1\t+\t.\tName=1;ID=1-25-phiX174;pvalue=4.88e-09;sequence=TATGTCTAATA;\n+phiX174\tfimo\tpolypeptide_motif\t1555\t1565\t82.5\t+\t.\tName=1;ID=1-26-phiX174;pvalue=5.58e-09;sequence=GACTTCTACCA;\n+phiX174\tfimo\tpolypeptide_motif\t4430\t4440\t82.5\t+\t.\tName=1;ID=1-27-phiX174;pvalue=5.62e-09;sequence=TGAGTATAATT;\n+phiX174\tfimo\tpolypeptide_motif\t1927\t1937\t82.3\t+\t.\tName=1;ID=1-28-phiX174;pvalue=5.82e-09;sequence=GACTTATACCG;\n+phiX174\tfimo\tpolypeptide_motif\t2981\t2991\t82.1\t+\t.\tName=1;ID=1-29-phiX174;pvalue=6.13e-09;sequence=CATGTCTAAAT;\n+phiX174\tfimo\tpolypeptide_motif\t4203\t4213\t 82\t+\t.\tName=1;ID=1-30-phiX174;pvalue=6.34e-09;sequence=GACGGCCATAA;\n+phiX174\tfimo\tpolypeptide_motif\t1669\t1679\t81.9\t+\t.\tName=1;ID=1-31-phiX174;pvalue=6.4e-09;sequence=TGGAGGTAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t3260\t3270\t81.5\t+\t.\tName=1;ID=1-32-phiX174;pvalue=7.01e-09;sequence=CGCTGATAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t3047\t3057\t81.3\t+\t.\tName=1;ID=1-33-phiX174;pvalue=7.4e-09;sequence=TACCGATAACA;\n+phiX174\tfimo\tpolypeptide_motif\t4176\t4186\t81.2\t+\t.\tName=1;ID=1-34-phiX174;pvalue=7.6e-09;sequence=GAGTTCGATAA;\n+phiX174\tfimo\tpolypeptide_motif\t4118\t4128\t81.1\t+\t.\tName=1;ID=1-35-phiX174;pvalue=7.7e-09;sequence=GATGGATAACC;\n+phiX174\tfimo\tpolypeptide_motif\t5370\t5380\t80.9\t+\t.\tName=1;ID=1-36-phiX174;p'..b'GT;\n+phiX174\tfimo\tpolypeptide_motif\t4217\t4227\t76.7\t+\t.\tName=1;ID=1-64-phiX174;pvalue=2.15e-08;sequence=TGCTTCTGACG;\n+phiX174\tfimo\tpolypeptide_motif\t4262\t4272\t76.6\t+\t.\tName=1;ID=1-65-phiX174;pvalue=2.18e-08;sequence=AATGGATGAAT;\n+phiX174\tfimo\tpolypeptide_motif\t3569\t3579\t76.5\t+\t.\tName=1;ID=1-66-phiX174;pvalue=2.26e-08;sequence=TATGGAAAACA;\n+phiX174\tfimo\tpolypeptide_motif\t194\t204\t76.4\t+\t.\tName=1;ID=1-67-phiX174;pvalue=2.29e-08;sequence=ATCAACTAACG;\n+phiX174\tfimo\tpolypeptide_motif\t131\t141\t 76\t+\t.\tName=1;ID=1-68-phiX174;pvalue=2.49e-08;sequence=AAATGAGAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t1491\t1501\t75.9\t+\t.\tName=1;ID=1-69-phiX174;pvalue=2.55e-08;sequence=GCCATCTCAAA;\n+phiX174\tfimo\tpolypeptide_motif\t434\t444\t75.7\t+\t.\tName=1;ID=1-70-phiX174;pvalue=2.67e-08;sequence=GGCCTCTATTA;\n+phiX174\tfimo\tpolypeptide_motif\t4565\t4575\t75.6\t+\t.\tName=1;ID=1-71-phiX174;pvalue=2.73e-08;sequence=TTGGTTTATCG;\n+phiX174\tfimo\tpolypeptide_motif\t102\t112\t75.6\t+\t.\tName=1;ID=1-72-phiX174;pvalue=2.75e-08;sequence=GAATTAAATCG;\n+phiX174\tfimo\tpolypeptide_motif\t903\t913\t75.5\t+\t.\tName=1;ID=1-73-phiX174;pvalue=2.82e-08;sequence=GAGGTACTAAA;\n+phiX174\tfimo\tpolypeptide_motif\t4748\t4758\t75.2\t+\t.\tName=1;ID=1-74-phiX174;pvalue=3.01e-08;sequence=TACAGCTAATG;\n+phiX174\tfimo\tpolypeptide_motif\t2622\t2632\t 75\t+\t.\tName=1;ID=1-75-phiX174;pvalue=3.16e-08;sequence=TGCTGATATTG;\n+phiX174\tfimo\tpolypeptide_motif\t467\t477\t74.7\t+\t.\tName=1;ID=1-76-phiX174;pvalue=3.35e-08;sequence=TTTGGATTTAA;\n+phiX174\tfimo\tpolypeptide_motif\t4033\t4043\t74.6\t+\t.\tName=1;ID=1-77-phiX174;pvalue=3.44e-08;sequence=AGCGTATCGAG;\n+phiX174\tfimo\tpolypeptide_motif\t1348\t1358\t74.6\t+\t.\tName=1;ID=1-78-phiX174;pvalue=3.46e-08;sequence=TACCAATAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t239\t249\t74.4\t+\t.\tName=1;ID=1-79-phiX174;pvalue=3.62e-08;sequence=AGTGGCTTAAT;\n+phiX174\tfimo\tpolypeptide_motif\t500\t510\t74.1\t+\t.\tName=1;ID=1-80-phiX174;pvalue=3.84e-08;sequence=GACGAGTAACA;\n+phiX174\tfimo\tpolypeptide_motif\t3001\t3011\t 74\t+\t.\tName=1;ID=1-81-phiX174;pvalue=3.93e-08;sequence=GCGGTCAAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t3776\t3786\t 74\t+\t.\tName=1;ID=1-82-phiX174;pvalue=3.98e-08;sequence=TATTTCTAATG;\n+phiX174\tfimo\tpolypeptide_motif\t2026\t2036\t73.9\t+\t.\tName=1;ID=1-83-phiX174;pvalue=4.06e-08;sequence=GAAGTTTAAGA;\n+phiX174\tfimo\tpolypeptide_motif\t4237\t4247\t73.8\t+\t.\tName=1;ID=1-84-phiX174;pvalue=4.12e-08;sequence=AGTTTGTATCT;\n+phiX174\tfimo\tpolypeptide_motif\t803\t813\t73.7\t+\t.\tName=1;ID=1-85-phiX174;pvalue=4.24e-08;sequence=AGAAGAAAACG;\n+phiX174\tfimo\tpolypeptide_motif\t3770\t3780\t73.6\t+\t.\tName=1;ID=1-86-phiX174;pvalue=4.35e-08;sequence=AAAGGATATTT;\n+phiX174\tfimo\tpolypeptide_motif\t3429\t3439\t73.5\t+\t.\tName=1;ID=1-87-phiX174;pvalue=4.45e-08;sequence=GAGATGCAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t99\t109\t73.5\t+\t.\tName=1;ID=1-88-phiX174;pvalue=4.48e-08;sequence=TACGAATTAAA;\n+phiX174\tfimo\tpolypeptide_motif\t67\t77\t73.2\t+\t.\tName=1;ID=1-89-phiX174;pvalue=4.78e-08;sequence=TCTTGATAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t5332\t5342\t72.9\t+\t.\tName=1;ID=1-90-phiX174;pvalue=5.13e-08;sequence=ATCTGCTCAAA;\n+phiX174\tfimo\tpolypeptide_motif\t277\t287\t72.9\t+\t.\tName=1;ID=1-91-phiX174;pvalue=5.14e-08;sequence=TTTAGATATGA;\n+phiX174\tfimo\tpolypeptide_motif\t4338\t4348\t72.8\t+\t.\tName=1;ID=1-92-phiX174;pvalue=5.18e-08;sequence=GGGGACGAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t3812\t3822\t72.8\t+\t.\tName=1;ID=1-93-phiX174;pvalue=5.28e-08;sequence=GGTTGATATTT;\n+phiX174\tfimo\tpolypeptide_motif\t1909\t1919\t72.6\t+\t.\tName=1;ID=1-94-phiX174;pvalue=5.51e-08;sequence=TAACGCTAAAG;\n+phiX174\tfimo\tpolypeptide_motif\t3000\t3010\t72.6\t+\t.\tName=1;ID=1-95-phiX174;pvalue=5.54e-08;sequence=GGCGGTCAAAA;\n+phiX174\tfimo\tpolypeptide_motif\t3891\t3901\t72.4\t+\t.\tName=1;ID=1-96-phiX174;pvalue=5.75e-08;sequence=ATTGGCTCTAA;\n+phiX174\tfimo\tpolypeptide_motif\t3079\t3089\t72.4\t+\t.\tName=1;ID=1-97-phiX174;pvalue=5.76e-08;sequence=CTGGTATTAAA;\n+phiX174\tfimo\tpolypeptide_motif\t37\t47\t72.4\t+\t.\tName=1;ID=1-98-phiX174;pvalue=5.79e-08;sequence=TTCGGATATTT;\n+phiX174\tfimo\tpolypeptide_motif\t380\t390\t72.2\t+\t.\tName=1;ID=1-99-phiX174;pvalue=6.01e-08;sequence=GTAAGAAATCA;\n'

diff -r e416c7c26977 -r d20e391eb22f test-data/fimo_output_html_1.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_html_1.html Tue Dec 22 17:02:11 2015 -0500

[

@@ -0,0 +1,100 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
+<html xmlns:cis="http://zlab.bu.edu/schema/cisml" xmlns:fimo="http://noble.gs.washington.edu/schema/cisml" xmlns:mem="http://noble.gs.washington.edu/meme">
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+<meta charset="UTF-8">
+<title>FIMO Results</title>
+<style type="text/css">
+td.left {text-align: left;}
+td.right {text-align: right; padding-right: 1cm;}
+</style>
+</head>
+<body bgcolor="#D5F0FF">
+<a name="top_buttons"></a>
+<hr>
+<table summary="buttons" align="left" cellspacing="0">
+<tr>
+<td bgcolor="#00FFFF"><a href="#database_and_motifs"><b>Database and Motifs</b></a></td>
+<td bgcolor="#DDFFDD"><a href="#sec_i"><b>High-scoring Motif Occurences</b></a></td>
+<td bgcolor="#DDDDFF"><a href="#debugging_information"><b>Debugging Information</b></a></td>
+</tr>
+</table>
+<br/>
+<br/>
+<hr/>
+<center><big><b>FIMO - Motif search tool</b></big></center>
+<hr>
+<p>
+FIMO version 4.11.0, (Release date: Thu Nov 26 17:48:49 2015 +1000)
+</p>
+<p>
+For further information on how to interpret these results
+or to get a copy of the FIMO software please access
+<a href="http://meme.nbcr.net">http://meme.nbcr.net</a></p>
+<p>If you use FIMO in your research, please cite the following paper:<br>
+Charles E. Grant, Timothy L. Bailey, and William Stafford Noble,
+"FIMO: Scanning for occurrences of a given motif",
+<i>Bioinformatics</i>, <b>27</b>(7):1017-1018, 2011.
+<a href="http://bioinformatics.oxfordjournals.org/content/27/7/1017">[full text]</a></p>
+<hr>
+<center><big><b><a name="database_and_motifs">DATABASE AND MOTIFS</a></b></big></center>
+<hr>
+<div style="padding-left: 0.75in; line-height: 1em; font-family: monospace;">
+<p>
+  DATABASE /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat
+  <br />
+  Database contains 1 sequences, 5386 residues
+</p>
+<p>
+  MOTIFS /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat (Protein)
+  <table>
+    <thead>
+      <tr>
+        <th style="border-bottom: 1px dashed;">MOTIF</th>
+        <th style="border-bottom: 1px dashed; padding-left: 1em;">WIDTH</th>
+        <th style="border-bottom: 1px dashed; padding-left: 1em;text-align:left;" >
+         BEST POSSIBLE MATCH
+        </th>
+      </tr>
+    </thead>
+    <tbody>
+      <tr>
+        <td style="text-align:right;">1</td>
+        <td style="text-align:right;padding-left: 1em;">11</td>
+        <td style="text-align:left;padding-left: 1em;">GGGGTATAAAA</td>
+       </tr>
+    </tbody>
+  </table>
+</p>
+<p>
+Random model letter frequencies (from non-redundant database):
+<br/>
+
+A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058
+L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064
+W 0.013 Y 0.033 </p>
+</div>
+<hr>
+<center><big><b><a name="sec_i">SECTION I: HIGH-SCORING MOTIF OCCURENCES</a></b></big></center>
+<hr>
+<ul>
+<li>
+There were 1937 motif occurences with a p-value less than 0.0001.
+<b>Only the most significant 1000 matches are shown here.</b>
+
+The full set of motif occurences can be seen in the
+tab-delimited plain text output file
+<a href="fimo.txt">fimo.txt</a>,
+the GFF file
+<a href="fimo.gff">fimo.gff</a>
+which may be suitable for uploading to the
+<a href="http://genome.ucsc.edu/cgi-bin/hgTables">UCSC Genome Table Browser</a>
+(assuming the FASTA input sequences included genomic coordinates in UCSC or Galaxy format),
+or the XML file
+<a href="fimo.xml">fimo.xml</a>.
+</li>
+<li>
+The p-value of a motif occurrence is defined as the
+probability of a random sequence of the same length as the motif
+matching that position of the sequence with as good or better a score.
+</li>

diff -r e416c7c26977 -r d20e391eb22f test-data/fimo_output_html_2.html
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_html_2.html Tue Dec 22 17:02:11 2015 -0500

[

diff -r e416c7c26977 -r d20e391eb22f test-data/fimo_output_interval_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_interval_1.txt Tue Dec 22 17:02:11 2015 -0500

@@ -0,0 +1,100 @@
+#chr start end pattern name score strand matched sequence p-value q-value
+phiX174 1387 1398 1 + + 1.25e-09 29.4024 6.36e-11
+phiX174 846 857 1 + + 1.25e-09 29.122 7.02e-11
+phiX174 2300 2311 1 + + 1.29e-09 27.6463 1.08e-10
+phiX174 5062 5073 1 + + 2.25e-09 25.5366 2.73e-10
+phiX174 988 999 1 + + 2.25e-09 25.3049 3.15e-10
+phiX174 4712 4723 1 + + 3.48e-09 23.622 7.74e-10
+phiX174 5047 5058 1 + + 3.48e-09 23.3293 8.51e-10
+phiX174 854 865 1 + + 3.48e-09 23.3049 8.64e-10
+phiX174 3154 3165 1 + + 3.48e-09 23.0366 9.76e-10
+phiX174 5008 5019 1 + + 3.48e-09 23.0366 9.76e-10
+phiX174 813 824 1 + + 4.14e-09 22.5854 1.28e-09
+phiX174 2831 2842 1 + + 4.23e-09 22.3415 1.42e-09
+phiX174 3829 3840 1 + + 4.68e-09 21.8293 1.7e-09
+phiX174 3559 3570 1 + + 4.82e-09 21.5976 1.89e-09
+phiX174 2881 2892 1 + + 5.46e-09 21.1951 2.29e-09
+phiX174 4452 4463 1 + + 5.75e-09 20.8902 2.58e-09
+phiX174 2492 2503 1 + + 5.79e-09 20.3415 3.06e-09
+phiX174 4103 4114 1 + + 5.79e-09 20.3171 3.08e-09
+phiX174 4954 4965 1 + + 5.79e-09 20.3171 3.08e-09
+phiX174 1884 1895 1 + + 6.45e-09 19.9268 3.61e-09
+phiX174 3375 3386 1 + + 6.48e-09 19.7683 3.81e-09
+phiX174 51 62 1 + + 6.58e-09 19.5732 4.06e-09
+phiX174 1389 1400 1 + + 6.61e-09 19.378 4.26e-09
+phiX174 2016 2027 1 + + 6.85e-09 19.0854 4.6e-09
+phiX174 999 1010 1 + + 6.97e-09 18.878 4.88e-09
+phiX174 1554 1565 1 + + 7.37e-09 18.439 5.58e-09
+phiX174 4429 4440 1 + + 7.37e-09 18.4268 5.62e-09
+phiX174 1926 1937 1 + + 7.37e-09 18.2927 5.82e-09
+phiX174 2980 2991 1 + + 7.37e-09 18.0732 6.13e-09
+phiX174 4202 4213 1 + + 7.37e-09 17.9268 6.34e-09
+phiX174 1668 1679 1 + + 7.37e-09 17.8659 6.4e-09
+phiX174 3259 3270 1 + + 7.82e-09 17.5 7.01e-09
+phiX174 3046 3057 1 + + 7.85e-09 17.2805 7.4e-09
+phiX174 4175 4186 1 + + 7.85e-09 17.1829 7.6e-09
+phiX174 4117 4128 1 + + 7.85e-09 17.1341 7.7e-09
+phiX174 5369 5380 1 + + 7.87e-09 16.9878 8.03e-09
+phiX174 1241 1252 1 + + 7.87e-09 16.5122 8.94e-09
+phiX174 2582 2593 1 + + 7.87e-09 16.5122 8.94e-09
+phiX174 697 708 1 + + 7.87e-09 16.4146 9.13e-09
+phiX174 2298 2309 1 + + 7.87e-09 16.3537 9.26e-09
+phiX174 4188 4199 1 + + 7.87e-09 16.1707 9.69e-09
+phiX174 274 285 1 + + 7.87e-09 16.0976 9.85e-09
+phiX174 1800 1811 1 + + 7.87e-09 16.0366 1e-08
+phiX174 1385 1396 1 + + 7.87e-09 15.9268 1.03e-08
+phiX174 1302 1313 1 + + 7.87e-09 15.9024 1.03e-08
+phiX174 3771 3782 1 + + 7.87e-09 15.878 1.04e-08
+phiX174 1287 1298 1 + + 7.87e-09 15.8659 1.04e-08
+phiX174 2576 2587 1 + + 7.87e-09 15.7683 1.08e-08
+phiX174 936 947 1 + + 7.87e-09 15.7561 1.08e-08
+phiX174 903 914 1 + + 7.93e-09 15.6585 1.11e-08
+phiX174 2278 2289 1 + + 7.93e-09 15.5854 1.13e-08
+phiX174 3163 3174 1 + + 7.98e-09 15.5 1.16e-08
+phiX174 23 34 1 + + 8.24e-09 15.3293 1.23e-08
+phiX174 837 848 1 + + 8.24e-09 15.2561 1.27e-08
+phiX174 852 863 1 + + 8.24e-09 15.2561 1.27e-08
+phiX174 1983 1994 1 + + 8.68e-09 15.0244 1.36e-08
+phiX174 0 11 1 + + 9.05e-09 14.8293 1.46e-08
+phiX174 4306 4317 1 + + 9.05e-09 14.7927 1.47e-08
+phiX174 4302 4313 1 + + 9.19e-09 14.6585 1.52e-08
+phiX174 5032 5043 1 + + 9.41e-09 14.561 1.58e-08
+phiX174 2578 2589 1 + + 1.01e-08 14.2927 1.73e-08
+phiX174 321 332 1 + + 1.05e-08 14.1951 1.82e-08
+phiX174 5000 5011 1 + + 1.19e-08 13.8902 2.09e-08
+phiX174 4216 4227 1 + + 1.2e-08 13.8171 2.15e-08
+phiX174 4261 4272 1 + + 1.2e-08 13.7805 2.18e-08
+phiX174 3568 3579 1 + + 1.22e-08 13.7073 2.26e-08
+phiX174 193 204 1 + + 1.22e-08 13.6829 2.29e-08
+phiX174 130 141 1 + + 1.31e-08 13.4756 2.49e-08
+phiX174 1490 1501 1 + + 1.32e-08 13.4024 2.55e-08
+phiX174 433 444 1 + + 1.36e-08 13.2805 2.67e-08
+phiX174 4564 4575 1 + + 1.36e-08 13.2439 2.73e-08
+phiX174 101 112 1 + + 1.36e-08 13.2195 2.75e-08
+phiX174 902 913 1 + + 1.38e-08 13.1463 2.82e-08
+phiX174 4747 4758 1 + + 1.45e-08 12.9756 3.01e-08
+phiX174 2621 2632 1 + + 1.5e-08 12.8659 3.16e-08
+phiX174 466 477 1 + + 1.57e-08 12.7317 3.35e-08
+phiX174 4032 4043 1 + + 1.58e-08 12.6829 3.44e-08
+phiX174 1347 1358 1 + + 1.58e-08 12.6707 3.46e-08
+phiX174 238 249 1 + + 1.64e-08 12.5732 3.62e-08
+phiX174 499 510 1 + + 1.71e-08 12.4634 3.84e-08
+phiX174 3000 3011 1 + + 1.73e-08 12.4146 3.93e-08
+phiX174 3775 3786 1 + + 1.73e-08 12.378 3.98e-08
+phiX174 2025 2036 1 + + 1.75e-08 12.3293 4.06e-08
+phiX174 4236 4247 1 + + 1.75e-08 12.3049 4.12e-08
+phiX174 802 813 1 + + 1.78e-08 12.2439 4.24e-08
+phiX174 3769 3780 1 + + 1.81e-08 12.1829 4.35e-08
+phiX174 3428 3439 1 + + 1.82e-08 12.122 4.45e-08
+phiX174 98 109 1 + + 1.82e-08 12.1098 4.48e-08
+phiX174 66 77 1 + + 1.92e-08 11.9268 4.78e-08
+phiX174 5331 5342 1 + + 2.01e-08 11.7195 5.13e-08
+phiX174 276 287 1 + + 2.01e-08 11.7073 5.14e-08
+phiX174 4337 4348 1 + + 2.01e-08 11.6951 5.18e-08
+phiX174 3811 3822 1 + + 2.03e-08 11.6585 5.28e-08
+phiX174 1908 1919 1 + + 2.08e-08 11.5488 5.51e-08
+phiX174 2999 3010 1 + + 2.08e-08 11.5366 5.54e-08
+phiX174 3890 3901 1 + + 2.11e-08 11.439 5.75e-08
+phiX174 3078 3089 1 + + 2.11e-08 11.4268 5.76e-08
+phiX174 36 47 1 + + 2.11e-08 11.4146 5.79e-08
+phiX174 379 390 1 + + 2.17e-08 11.3293 6.01e-08

diff -r e416c7c26977 -r d20e391eb22f test-data/fimo_output_interval_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_interval_2.txt Tue Dec 22 17:02:11 2015 -0500

@@ -0,0 +1,100 @@
+#chr start end pattern name score strand matched sequence p-value q-value
+phiX174 1387 1398 1 + + 0 29.4024 6.36e-11
+phiX174 846 857 1 + + 0 29.122 7.02e-11
+phiX174 2300 2311 1 + + 0 27.6463 1.08e-10
+phiX174 5062 5073 1 + + 0 25.5366 2.73e-10
+phiX174 988 999 1 + + 0 25.3049 3.15e-10
+phiX174 4712 4723 1 + + 0 23.622 7.74e-10
+phiX174 5047 5058 1 + + 0 23.3293 8.51e-10
+phiX174 854 865 1 + + 0 23.3049 8.64e-10
+phiX174 3154 3165 1 + + 0 23.0366 9.76e-10
+phiX174 5008 5019 1 + + 0 23.0366 9.76e-10
+phiX174 813 824 1 + + 0 22.5854 1.28e-09
+phiX174 2831 2842 1 + + 0 22.3415 1.42e-09
+phiX174 3829 3840 1 + + 0 21.8293 1.7e-09
+phiX174 3559 3570 1 + + 0 21.5976 1.89e-09
+phiX174 2881 2892 1 + + 0 21.1951 2.29e-09
+phiX174 4452 4463 1 + + 0 20.8902 2.58e-09
+phiX174 2492 2503 1 + + 0 20.3415 3.06e-09
+phiX174 4103 4114 1 + + 0 20.3171 3.08e-09
+phiX174 4954 4965 1 + + 0 20.3171 3.08e-09
+phiX174 1884 1895 1 + + 0 19.9268 3.61e-09
+phiX174 3375 3386 1 + + 0 19.7683 3.81e-09
+phiX174 51 62 1 + + 0 19.5732 4.06e-09
+phiX174 1389 1400 1 + + 0 19.378 4.26e-09
+phiX174 2016 2027 1 + + 0 19.0854 4.6e-09
+phiX174 999 1010 1 + + 0 18.878 4.88e-09
+phiX174 1554 1565 1 + + 0 18.439 5.58e-09
+phiX174 4429 4440 1 + + 0 18.4268 5.62e-09
+phiX174 1926 1937 1 + + 0 18.2927 5.82e-09
+phiX174 2980 2991 1 + + 0 18.0732 6.13e-09
+phiX174 4202 4213 1 + + 0 17.9268 6.34e-09
+phiX174 1668 1679 1 + + 0 17.8659 6.4e-09
+phiX174 3259 3270 1 + + 0 17.5 7.01e-09
+phiX174 3046 3057 1 + + 0 17.2805 7.4e-09
+phiX174 4175 4186 1 + + 0 17.1829 7.6e-09
+phiX174 4117 4128 1 + + 0 17.1341 7.7e-09
+phiX174 5369 5380 1 + + 0 16.9878 8.03e-09
+phiX174 1241 1252 1 + + 0 16.5122 8.94e-09
+phiX174 2582 2593 1 + + 0 16.5122 8.94e-09
+phiX174 697 708 1 + + 0 16.4146 9.13e-09
+phiX174 2298 2309 1 + + 0 16.3537 9.26e-09
+phiX174 4188 4199 1 + + 0 16.1707 9.69e-09
+phiX174 274 285 1 + + 0 16.0976 9.85e-09
+phiX174 1800 1811 1 + + 0 16.0366 1e-08
+phiX174 1385 1396 1 + + 0 15.9268 1.03e-08
+phiX174 1302 1313 1 + + 0 15.9024 1.03e-08
+phiX174 3771 3782 1 + + 0 15.878 1.04e-08
+phiX174 1287 1298 1 + + 0 15.8659 1.04e-08
+phiX174 2576 2587 1 + + 0 15.7683 1.08e-08
+phiX174 936 947 1 + + 0 15.7561 1.08e-08
+phiX174 903 914 1 + + 0 15.6585 1.11e-08
+phiX174 2278 2289 1 + + 0 15.5854 1.13e-08
+phiX174 3163 3174 1 + + 0 15.5 1.16e-08
+phiX174 23 34 1 + + 0 15.3293 1.23e-08
+phiX174 837 848 1 + + 0 15.2561 1.27e-08
+phiX174 852 863 1 + + 0 15.2561 1.27e-08
+phiX174 1983 1994 1 + + 0 15.0244 1.36e-08
+phiX174 0 11 1 + + 0 14.8293 1.46e-08
+phiX174 4306 4317 1 + + 0 14.7927 1.47e-08
+phiX174 4302 4313 1 + + 0 14.6585 1.52e-08
+phiX174 5032 5043 1 + + 0 14.561 1.58e-08
+phiX174 2578 2589 1 + + 0 14.2927 1.73e-08
+phiX174 321 332 1 + + 0 14.1951 1.82e-08
+phiX174 5000 5011 1 + + 0 13.8902 2.09e-08
+phiX174 4216 4227 1 + + 0 13.8171 2.15e-08
+phiX174 4261 4272 1 + + 0 13.7805 2.18e-08
+phiX174 3568 3579 1 + + 0 13.7073 2.26e-08
+phiX174 193 204 1 + + 0 13.6829 2.29e-08
+phiX174 130 141 1 + + 0 13.4756 2.49e-08
+phiX174 1490 1501 1 + + 0 13.4024 2.55e-08
+phiX174 433 444 1 + + 0 13.2805 2.67e-08
+phiX174 4564 4575 1 + + 0 13.2439 2.73e-08
+phiX174 101 112 1 + + 0 13.2195 2.75e-08
+phiX174 902 913 1 + + 0 13.1463 2.82e-08
+phiX174 4747 4758 1 + + 0 12.9756 3.01e-08
+phiX174 2621 2632 1 + + 0 12.8659 3.16e-08
+phiX174 466 477 1 + + 0 12.7317 3.35e-08
+phiX174 4032 4043 1 + + 0 12.6829 3.44e-08
+phiX174 1347 1358 1 + + 0 12.6707 3.46e-08
+phiX174 238 249 1 + + 0 12.5732 3.62e-08
+phiX174 499 510 1 + + 0 12.4634 3.84e-08
+phiX174 3000 3011 1 + + 0 12.4146 3.93e-08
+phiX174 3775 3786 1 + + 0 12.378 3.98e-08
+phiX174 2025 2036 1 + + 0 12.3293 4.06e-08
+phiX174 4236 4247 1 + + 0 12.3049 4.12e-08
+phiX174 802 813 1 + + 0 12.2439 4.24e-08
+phiX174 3769 3780 1 + + 0 12.1829 4.35e-08
+phiX174 3428 3439 1 + + 0 12.122 4.45e-08
+phiX174 98 109 1 + + 0 12.1098 4.48e-08
+phiX174 66 77 1 + + 0 11.9268 4.78e-08
+phiX174 5331 5342 1 + + 0 11.7195 5.13e-08
+phiX174 276 287 1 + + 0 11.7073 5.14e-08
+phiX174 4337 4348 1 + + 0 11.6951 5.18e-08
+phiX174 3811 3822 1 + + 0 11.6585 5.28e-08
+phiX174 1908 1919 1 + + 0 11.5488 5.51e-08
+phiX174 2999 3010 1 + + 0 11.5366 5.54e-08
+phiX174 3890 3901 1 + + 0 11.439 5.75e-08
+phiX174 3078 3089 1 + + 0 11.4268 5.76e-08
+phiX174 36 47 1 + + 0 11.4146 5.79e-08
+phiX174 379 390 1 + + 0 11.3293 6.01e-08

diff -r e416c7c26977 -r d20e391eb22f test-data/fimo_output_txt_1.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_txt_1.txt Tue Dec 22 17:02:11 2015 -0500

@@ -0,0 +1,100 @@
+#pattern name sequence name start stop strand score p-value q-value matched sequence
+1 phiX174 1388 1398 + 29.4024 6.36e-11 1.25e-09 AATATCTATAA
+1 phiX174 847 857 + 29.122 7.02e-11 1.25e-09 AATGTCTAAAG
+1 phiX174 2301 2311 + 27.6463 1.08e-10 1.29e-09 AGGTTATAACG
+1 phiX174 5063 5073 + 25.5366 2.73e-10 2.25e-09 AGGAGCTAAAG
+1 phiX174 989 999 + 25.3049 3.15e-10 2.25e-09 TGAGGATAAAT
+1 phiX174 4713 4723 + 23.622 7.74e-10 3.48e-09 GACTGCTATCA
+1 phiX174 5048 5058 + 23.3293 8.51e-10 3.48e-09 TGCTGCTAAAG
+1 phiX174 855 865 + 23.3049 8.64e-10 3.48e-09 AAGGTAAAAAA
+1 phiX174 3155 3165 + 23.0366 9.76e-10 3.48e-09 TATGGCTAAAG
+1 phiX174 5009 5019 + 23.0366 9.76e-10 3.48e-09 TGTGGCTAAAT
+1 phiX174 814 824 + 22.5854 1.28e-09 4.14e-09 TGCGTCAAAAA
+1 phiX174 2832 2842 + 22.3415 1.42e-09 4.23e-09 TTGGTCTAACT
+1 phiX174 3830 3840 + 21.8293 1.7e-09 4.68e-09 TATTGATAAAG
+1 phiX174 3560 3570 + 21.5976 1.89e-09 4.82e-09 TGCGTCTATTA
+1 phiX174 2882 2892 + 21.1951 2.29e-09 5.46e-09 AGGTTATTAAA
+1 phiX174 4453 4463 + 20.8902 2.58e-09 5.75e-09 AAGGTATTAAG
+1 phiX174 2493 2503 + 20.3415 3.06e-09 5.79e-09 GACACCTAAAG
+1 phiX174 4104 4114 + 20.3171 3.08e-09 5.79e-09 GGCTTCCATAA
+1 phiX174 4955 4965 + 20.3171 3.08e-09 5.79e-09 TGATGCTAAAG
+1 phiX174 1885 1895 + 19.9268 3.61e-09 6.45e-09 TGCGACTAAAG
+1 phiX174 3376 3386 + 19.7683 3.81e-09 6.48e-09 AGAATCAAAAA
+1 phiX174 52 62 + 19.5732 4.06e-09 6.58e-09 TGAGTCGAAAA
+1 phiX174 1390 1400 + 19.378 4.26e-09 6.61e-09 TATCTATAACA
+1 phiX174 2017 2027 + 19.0854 4.6e-09 6.85e-09 TTCGTCTAAGA
+1 phiX174 1000 1010 + 18.878 4.88e-09 6.97e-09 TATGTCTAATA
+1 phiX174 1555 1565 + 18.439 5.58e-09 7.37e-09 GACTTCTACCA
+1 phiX174 4430 4440 + 18.4268 5.62e-09 7.37e-09 TGAGTATAATT
+1 phiX174 1927 1937 + 18.2927 5.82e-09 7.37e-09 GACTTATACCG
+1 phiX174 2981 2991 + 18.0732 6.13e-09 7.37e-09 CATGTCTAAAT
+1 phiX174 4203 4213 + 17.9268 6.34e-09 7.37e-09 GACGGCCATAA
+1 phiX174 1669 1679 + 17.8659 6.4e-09 7.37e-09 TGGAGGTAAAA
+1 phiX174 3260 3270 + 17.5 7.01e-09 7.82e-09 CGCTGATAAAG
+1 phiX174 3047 3057 + 17.2805 7.4e-09 7.85e-09 TACCGATAACA
+1 phiX174 4176 4186 + 17.1829 7.6e-09 7.85e-09 GAGTTCGATAA
+1 phiX174 4118 4128 + 17.1341 7.7e-09 7.85e-09 GATGGATAACC
+1 phiX174 5370 5380 + 16.9878 8.03e-09 7.87e-09 GGCGTATCCAA
+1 phiX174 1242 1252 + 16.5122 8.94e-09 7.87e-09 AGTGGATTAAG
+1 phiX174 2583 2593 + 16.5122 8.94e-09 7.87e-09 TACATCTGTCA
+1 phiX174 698 708 + 16.4146 9.13e-09 7.87e-09 TACGGAAAACA
+1 phiX174 2299 2309 + 16.3537 9.26e-09 7.87e-09 TGAGGTTATAA
+1 phiX174 4189 4199 + 16.1707 9.69e-09 7.87e-09 GTGATATGTAT
+1 phiX174 275 285 + 16.0976 9.85e-09 7.87e-09 GGTTTAGATAT
+1 phiX174 1801 1811 + 16.0366 1e-08 7.87e-09 GACCTATAAAC
+1 phiX174 1386 1396 + 15.9268 1.03e-08 7.87e-09 TGAATATCTAT
+1 phiX174 1303 1313 + 15.9024 1.03e-08 7.87e-09 TGGTTATATTG
+1 phiX174 3772 3782 + 15.878 1.04e-08 7.87e-09 AGGATATTTCT
+1 phiX174 1288 1298 + 15.8659 1.04e-08 7.87e-09 GACTGTTAACA
+1 phiX174 2577 2587 + 15.7683 1.08e-08 7.87e-09 GATGGATACAT
+1 phiX174 937 947 + 15.7561 1.08e-08 7.87e-09 TTGGTATGTAG
+1 phiX174 904 914 + 15.6585 1.11e-08 7.93e-09 AGGTACTAAAG
+1 phiX174 2279 2289 + 15.5854 1.13e-08 7.93e-09 TCGTGATAAAA
+1 phiX174 3164 3174 + 15.5 1.16e-08 7.98e-09 AGCTGGTAAAG
+1 phiX174 24 34 + 15.3293 1.23e-08 8.24e-09 AGAAGTTAACA
+1 phiX174 838 848 + 15.2561 1.27e-08 8.24e-09 GAGTGATGTAA
+1 phiX174 853 863 + 15.2561 1.27e-08 8.24e-09 TAAAGGTAAAA
+1 phiX174 1984 1994 + 15.0244 1.36e-08 8.68e-09 AATTTCTATGA
+1 phiX174 1 11 + 14.8293 1.46e-08 9.05e-09 GAGTTTTATCG
+1 phiX174 4307 4317 + 14.7927 1.47e-08 9.05e-09 TATTAATAACA
+1 phiX174 4303 4313 + 14.6585 1.52e-08 9.19e-09 TTGATATTAAT
+1 phiX174 5033 5043 + 14.561 1.58e-08 9.41e-09 GTCAGATATGG
+1 phiX174 2579 2589 + 14.2927 1.73e-08 1.01e-08 TGGATACATCT
+1 phiX174 322 332 + 14.1951 1.82e-08 1.05e-08 GACATTTTAAA
+1 phiX174 5001 5011 + 13.8902 2.09e-08 1.19e-08 GGTTTCTATGT
+1 phiX174 4217 4227 + 13.8171 2.15e-08 1.2e-08 TGCTTCTGACG
+1 phiX174 4262 4272 + 13.7805 2.18e-08 1.2e-08 AATGGATGAAT
+1 phiX174 3569 3579 + 13.7073 2.26e-08 1.22e-08 TATGGAAAACA
+1 phiX174 194 204 + 13.6829 2.29e-08 1.22e-08 ATCAACTAACG
+1 phiX174 131 141 + 13.4756 2.49e-08 1.31e-08 AAATGAGAAAA
+1 phiX174 1491 1501 + 13.4024 2.55e-08 1.32e-08 GCCATCTCAAA
+1 phiX174 434 444 + 13.2805 2.67e-08 1.36e-08 GGCCTCTATTA
+1 phiX174 4565 4575 + 13.2439 2.73e-08 1.36e-08 TTGGTTTATCG
+1 phiX174 102 112 + 13.2195 2.75e-08 1.36e-08 GAATTAAATCG
+1 phiX174 903 913 + 13.1463 2.82e-08 1.38e-08 GAGGTACTAAA
+1 phiX174 4748 4758 + 12.9756 3.01e-08 1.45e-08 TACAGCTAATG
+1 phiX174 2622 2632 + 12.8659 3.16e-08 1.5e-08 TGCTGATATTG
+1 phiX174 467 477 + 12.7317 3.35e-08 1.57e-08 TTTGGATTTAA
+1 phiX174 4033 4043 + 12.6829 3.44e-08 1.58e-08 AGCGTATCGAG
+1 phiX174 1348 1358 + 12.6707 3.46e-08 1.58e-08 TACCAATAAAA
+1 phiX174 239 249 + 12.5732 3.62e-08 1.64e-08 AGTGGCTTAAT
+1 phiX174 500 510 + 12.4634 3.84e-08 1.71e-08 GACGAGTAACA
+1 phiX174 3001 3011 + 12.4146 3.93e-08 1.73e-08 GCGGTCAAAAA
+1 phiX174 3776 3786 + 12.378 3.98e-08 1.73e-08 TATTTCTAATG
+1 phiX174 2026 2036 + 12.3293 4.06e-08 1.75e-08 GAAGTTTAAGA
+1 phiX174 4237 4247 + 12.3049 4.12e-08 1.75e-08 AGTTTGTATCT
+1 phiX174 803 813 + 12.2439 4.24e-08 1.78e-08 AGAAGAAAACG
+1 phiX174 3770 3780 + 12.1829 4.35e-08 1.81e-08 AAAGGATATTT
+1 phiX174 3429 3439 + 12.122 4.45e-08 1.82e-08 GAGATGCAAAA
+1 phiX174 99 109 + 12.1098 4.48e-08 1.82e-08 TACGAATTAAA
+1 phiX174 67 77 + 11.9268 4.78e-08 1.92e-08 TCTTGATAAAG
+1 phiX174 5332 5342 + 11.7195 5.13e-08 2.01e-08 ATCTGCTCAAA
+1 phiX174 277 287 + 11.7073 5.14e-08 2.01e-08 TTTAGATATGA
+1 phiX174 4338 4348 + 11.6951 5.18e-08 2.01e-08 GGGGACGAAAA
+1 phiX174 3812 3822 + 11.6585 5.28e-08 2.03e-08 GGTTGATATTT
+1 phiX174 1909 1919 + 11.5488 5.51e-08 2.08e-08 TAACGCTAAAG
+1 phiX174 3000 3010 + 11.5366 5.54e-08 2.08e-08 GGCGGTCAAAA
+1 phiX174 3891 3901 + 11.439 5.75e-08 2.11e-08 ATTGGCTCTAA
+1 phiX174 3079 3089 + 11.4268 5.76e-08 2.11e-08 CTGGTATTAAA
+1 phiX174 37 47 + 11.4146 5.79e-08 2.11e-08 TTCGGATATTT
+1 phiX174 380 390 + 11.3293 6.01e-08 2.17e-08 GTAAGAAATCA

diff -r e416c7c26977 -r d20e391eb22f test-data/fimo_output_txt_2.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_txt_2.txt Tue Dec 22 17:02:11 2015 -0500

@@ -0,0 +1,100 @@
+#pattern name sequence name start stop strand score p-value q-value matched sequence
+1 phiX174 1388 1398 + 29.4024 6.36e-11 0 AATATCTATAA
+1 phiX174 847 857 + 29.122 7.02e-11 0 AATGTCTAAAG
+1 phiX174 2301 2311 + 27.6463 1.08e-10 0 AGGTTATAACG
+1 phiX174 5063 5073 + 25.5366 2.73e-10 0 AGGAGCTAAAG
+1 phiX174 989 999 + 25.3049 3.15e-10 0 TGAGGATAAAT
+1 phiX174 4713 4723 + 23.622 7.74e-10 0 GACTGCTATCA
+1 phiX174 5048 5058 + 23.3293 8.51e-10 0 TGCTGCTAAAG
+1 phiX174 855 865 + 23.3049 8.64e-10 0 AAGGTAAAAAA
+1 phiX174 3155 3165 + 23.0366 9.76e-10 0 TATGGCTAAAG
+1 phiX174 5009 5019 + 23.0366 9.76e-10 0 TGTGGCTAAAT
+1 phiX174 814 824 + 22.5854 1.28e-09 0 TGCGTCAAAAA
+1 phiX174 2832 2842 + 22.3415 1.42e-09 0 TTGGTCTAACT
+1 phiX174 3830 3840 + 21.8293 1.7e-09 0 TATTGATAAAG
+1 phiX174 3560 3570 + 21.5976 1.89e-09 0 TGCGTCTATTA
+1 phiX174 2882 2892 + 21.1951 2.29e-09 0 AGGTTATTAAA
+1 phiX174 4453 4463 + 20.8902 2.58e-09 0 AAGGTATTAAG
+1 phiX174 2493 2503 + 20.3415 3.06e-09 0 GACACCTAAAG
+1 phiX174 4104 4114 + 20.3171 3.08e-09 0 GGCTTCCATAA
+1 phiX174 4955 4965 + 20.3171 3.08e-09 0 TGATGCTAAAG
+1 phiX174 1885 1895 + 19.9268 3.61e-09 0 TGCGACTAAAG
+1 phiX174 3376 3386 + 19.7683 3.81e-09 0 AGAATCAAAAA
+1 phiX174 52 62 + 19.5732 4.06e-09 0 TGAGTCGAAAA
+1 phiX174 1390 1400 + 19.378 4.26e-09 0 TATCTATAACA
+1 phiX174 2017 2027 + 19.0854 4.6e-09 0 TTCGTCTAAGA
+1 phiX174 1000 1010 + 18.878 4.88e-09 0 TATGTCTAATA
+1 phiX174 1555 1565 + 18.439 5.58e-09 0 GACTTCTACCA
+1 phiX174 4430 4440 + 18.4268 5.62e-09 0 TGAGTATAATT
+1 phiX174 1927 1937 + 18.2927 5.82e-09 0 GACTTATACCG
+1 phiX174 2981 2991 + 18.0732 6.13e-09 0 CATGTCTAAAT
+1 phiX174 4203 4213 + 17.9268 6.34e-09 0 GACGGCCATAA
+1 phiX174 1669 1679 + 17.8659 6.4e-09 0 TGGAGGTAAAA
+1 phiX174 3260 3270 + 17.5 7.01e-09 0 CGCTGATAAAG
+1 phiX174 3047 3057 + 17.2805 7.4e-09 0 TACCGATAACA
+1 phiX174 4176 4186 + 17.1829 7.6e-09 0 GAGTTCGATAA
+1 phiX174 4118 4128 + 17.1341 7.7e-09 0 GATGGATAACC
+1 phiX174 5370 5380 + 16.9878 8.03e-09 0 GGCGTATCCAA
+1 phiX174 1242 1252 + 16.5122 8.94e-09 0 AGTGGATTAAG
+1 phiX174 2583 2593 + 16.5122 8.94e-09 0 TACATCTGTCA
+1 phiX174 698 708 + 16.4146 9.13e-09 0 TACGGAAAACA
+1 phiX174 2299 2309 + 16.3537 9.26e-09 0 TGAGGTTATAA
+1 phiX174 4189 4199 + 16.1707 9.69e-09 0 GTGATATGTAT
+1 phiX174 275 285 + 16.0976 9.85e-09 0 GGTTTAGATAT
+1 phiX174 1801 1811 + 16.0366 1e-08 0 GACCTATAAAC
+1 phiX174 1386 1396 + 15.9268 1.03e-08 0 TGAATATCTAT
+1 phiX174 1303 1313 + 15.9024 1.03e-08 0 TGGTTATATTG
+1 phiX174 3772 3782 + 15.878 1.04e-08 0 AGGATATTTCT
+1 phiX174 1288 1298 + 15.8659 1.04e-08 0 GACTGTTAACA
+1 phiX174 2577 2587 + 15.7683 1.08e-08 0 GATGGATACAT
+1 phiX174 937 947 + 15.7561 1.08e-08 0 TTGGTATGTAG
+1 phiX174 904 914 + 15.6585 1.11e-08 0 AGGTACTAAAG
+1 phiX174 2279 2289 + 15.5854 1.13e-08 0 TCGTGATAAAA
+1 phiX174 3164 3174 + 15.5 1.16e-08 0 AGCTGGTAAAG
+1 phiX174 24 34 + 15.3293 1.23e-08 0 AGAAGTTAACA
+1 phiX174 838 848 + 15.2561 1.27e-08 0 GAGTGATGTAA
+1 phiX174 853 863 + 15.2561 1.27e-08 0 TAAAGGTAAAA
+1 phiX174 1984 1994 + 15.0244 1.36e-08 0 AATTTCTATGA
+1 phiX174 1 11 + 14.8293 1.46e-08 0 GAGTTTTATCG
+1 phiX174 4307 4317 + 14.7927 1.47e-08 0 TATTAATAACA
+1 phiX174 4303 4313 + 14.6585 1.52e-08 0 TTGATATTAAT
+1 phiX174 5033 5043 + 14.561 1.58e-08 0 GTCAGATATGG
+1 phiX174 2579 2589 + 14.2927 1.73e-08 0 TGGATACATCT
+1 phiX174 322 332 + 14.1951 1.82e-08 0 GACATTTTAAA
+1 phiX174 5001 5011 + 13.8902 2.09e-08 0 GGTTTCTATGT
+1 phiX174 4217 4227 + 13.8171 2.15e-08 0 TGCTTCTGACG
+1 phiX174 4262 4272 + 13.7805 2.18e-08 0 AATGGATGAAT
+1 phiX174 3569 3579 + 13.7073 2.26e-08 0 TATGGAAAACA
+1 phiX174 194 204 + 13.6829 2.29e-08 0 ATCAACTAACG
+1 phiX174 131 141 + 13.4756 2.49e-08 0 AAATGAGAAAA
+1 phiX174 1491 1501 + 13.4024 2.55e-08 0 GCCATCTCAAA
+1 phiX174 434 444 + 13.2805 2.67e-08 0 GGCCTCTATTA
+1 phiX174 4565 4575 + 13.2439 2.73e-08 0 TTGGTTTATCG
+1 phiX174 102 112 + 13.2195 2.75e-08 0 GAATTAAATCG
+1 phiX174 903 913 + 13.1463 2.82e-08 0 GAGGTACTAAA
+1 phiX174 4748 4758 + 12.9756 3.01e-08 0 TACAGCTAATG
+1 phiX174 2622 2632 + 12.8659 3.16e-08 0 TGCTGATATTG
+1 phiX174 467 477 + 12.7317 3.35e-08 0 TTTGGATTTAA
+1 phiX174 4033 4043 + 12.6829 3.44e-08 0 AGCGTATCGAG
+1 phiX174 1348 1358 + 12.6707 3.46e-08 0 TACCAATAAAA
+1 phiX174 239 249 + 12.5732 3.62e-08 0 AGTGGCTTAAT
+1 phiX174 500 510 + 12.4634 3.84e-08 0 GACGAGTAACA
+1 phiX174 3001 3011 + 12.4146 3.93e-08 0 GCGGTCAAAAA
+1 phiX174 3776 3786 + 12.378 3.98e-08 0 TATTTCTAATG
+1 phiX174 2026 2036 + 12.3293 4.06e-08 0 GAAGTTTAAGA
+1 phiX174 4237 4247 + 12.3049 4.12e-08 0 AGTTTGTATCT
+1 phiX174 803 813 + 12.2439 4.24e-08 0 AGAAGAAAACG
+1 phiX174 3770 3780 + 12.1829 4.35e-08 0 AAAGGATATTT
+1 phiX174 3429 3439 + 12.122 4.45e-08 0 GAGATGCAAAA
+1 phiX174 99 109 + 12.1098 4.48e-08 0 TACGAATTAAA
+1 phiX174 67 77 + 11.9268 4.78e-08 0 TCTTGATAAAG
+1 phiX174 5332 5342 + 11.7195 5.13e-08 0 ATCTGCTCAAA
+1 phiX174 277 287 + 11.7073 5.14e-08 0 TTTAGATATGA
+1 phiX174 4338 4348 + 11.6951 5.18e-08 0 GGGGACGAAAA
+1 phiX174 3812 3822 + 11.6585 5.28e-08 0 GGTTGATATTT
+1 phiX174 1909 1919 + 11.5488 5.51e-08 0 TAACGCTAAAG
+1 phiX174 3000 3010 + 11.5366 5.54e-08 0 GGCGGTCAAAA
+1 phiX174 3891 3901 + 11.439 5.75e-08 0 ATTGGCTCTAA
+1 phiX174 3079 3089 + 11.4268 5.76e-08 0 CTGGTATTAAA
+1 phiX174 37 47 + 11.4146 5.79e-08 0 TTCGGATATTT
+1 phiX174 380 390 + 11.3293 6.01e-08 0 GTAAGAAATCA

diff -r e416c7c26977 -r d20e391eb22f test-data/fimo_output_xml_1.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_xml_1.xml Tue Dec 22 17:02:11 2015 -0500

@@ -0,0 +1,74 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+
+<fimo version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000">
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
+>
+<command-line>fimo --o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1973/dataset_2713_files --verbosity 1 /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</command-line>
+<settings>
+<setting name="output directory">/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1973/dataset_2713_files</setting>
+<setting name="MEME file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat</setting>
+<setting name="sequence file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</setting>
+<setting name="allow clobber">false</setting>
+<setting name="compute q-values">true</setting>
+<setting name="parse genomic coord.">false</setting>
+<setting name="text only">false</setting>
+<setting name="scan both strands">false</setting>
+<setting name="output threshold">0.0001</setting>
+<setting name="threshold type">p-value</setting>
+<setting name="max stored scores">100000</setting>
+<setting name="pseudocount">0.1</setting>
+<setting name="verbosity">1</setting>
+</settings>
+<sequence-data num-sequences="1" num-residues="5386" />
+<alphabet name="Protein" like="protein">
+<letter id="A" symbol="A" name="Alanine" colour="0000CC"/>
+<letter id="C" symbol="C" name="Cysteine" colour="0000CC"/>
+<letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/>
+<letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/>
+<letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/>
+<letter id="G" symbol="G" name="Glycine" colour="FFB300"/>
+<letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/>
+<letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/>
+<letter id="K" symbol="K" name="Lysine" colour="CC0000"/>
+<letter id="L" symbol="L" name="Leucine" colour="0000CC"/>
+<letter id="M" symbol="M" name="Methionine" colour="0000CC"/>
+<letter id="N" symbol="N" name="Asparagine" colour="008000"/>
+<letter id="P" symbol="P" name="Proline" colour="FFFF00"/>
+<letter id="Q" symbol="Q" name="Glutamine" colour="008000"/>
+<letter id="R" symbol="R" name="Arginine" colour="CC0000"/>
+<letter id="S" symbol="S" name="Serine" colour="008000"/>
+<letter id="T" symbol="T" name="Threonine" colour="008000"/>
+<letter id="V" symbol="V" name="Valine" colour="0000CC"/>
+<letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/>
+<letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/>
+<letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/>
+<letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/>
+<letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/>
+<letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/>
+</alphabet>
+<motif name="1" width="11" best-possible-match="GGGGTATAAAA"/>
+<background source="non-redundant database">
+<value letter="A">0.073</value>
+<value letter="C">0.018</value>
+<value letter="D">0.052</value>
+<value letter="E">0.062</value>
+<value letter="F">0.040</value>
+<value letter="G">0.069</value>
+<value letter="H">0.022</value>
+<value letter="I">0.056</value>
+<value letter="K">0.058</value>
+<value letter="L">0.092</value>
+<value letter="M">0.023</value>
+<value letter="N">0.046</value>
+<value letter="P">0.051</value>
+<value letter="Q">0.041</value>
+<value letter="R">0.052</value>
+<value letter="S">0.074</value>
+<value letter="T">0.059</value>
+<value letter="V">0.064</value>
+<value letter="W">0.013</value>
+<value letter="Y">0.033</value>
+</background>
+<cisml-file>cisml.xml</cisml-file>
+</fimo>

diff -r e416c7c26977 -r d20e391eb22f test-data/fimo_output_xml_2.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/fimo_output_xml_2.xml Tue Dec 22 17:02:11 2015 -0500

@@ -0,0 +1,74 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+
+<fimo version="4.11.0" release="Thu Nov 26 17:48:49 2015 +1000">
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xsi:schemaLocation= xmlns:fimo="http://noble.gs.washington.edu/schema/fimo"
+>
+<command-line>fimo --alpha 1.000000 --max-stored-scores 100000 --motif-pseudo 0.100000 --no-qvalue --thresh 0.000100 --o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1978/dataset_2738_files --verbosity 1 /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</command-line>
+<settings>
+<setting name="output directory">/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1978/dataset_2738_files</setting>
+<setting name="MEME file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2540.dat</setting>
+<setting name="sequence file name">/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2541.dat</setting>
+<setting name="allow clobber">false</setting>
+<setting name="compute q-values">false</setting>
+<setting name="parse genomic coord.">false</setting>
+<setting name="text only">false</setting>
+<setting name="scan both strands">false</setting>
+<setting name="output threshold">0.0001</setting>
+<setting name="threshold type">p-value</setting>
+<setting name="max stored scores">100000</setting>
+<setting name="pseudocount">0.1</setting>
+<setting name="verbosity">1</setting>
+</settings>
+<sequence-data num-sequences="1" num-residues="5386" />
+<alphabet name="Protein" like="protein">
+<letter id="A" symbol="A" name="Alanine" colour="0000CC"/>
+<letter id="C" symbol="C" name="Cysteine" colour="0000CC"/>
+<letter id="D" symbol="D" name="Aspartic acid" colour="FF00FF"/>
+<letter id="E" symbol="E" name="Glutamic acid" colour="FF00FF"/>
+<letter id="F" symbol="F" name="Phenylalanine" colour="0000CC"/>
+<letter id="G" symbol="G" name="Glycine" colour="FFB300"/>
+<letter id="H" symbol="H" name="Histidine" colour="FFCCCC"/>
+<letter id="I" symbol="I" name="Isoleucine" colour="0000CC"/>
+<letter id="K" symbol="K" name="Lysine" colour="CC0000"/>
+<letter id="L" symbol="L" name="Leucine" colour="0000CC"/>
+<letter id="M" symbol="M" name="Methionine" colour="0000CC"/>
+<letter id="N" symbol="N" name="Asparagine" colour="008000"/>
+<letter id="P" symbol="P" name="Proline" colour="FFFF00"/>
+<letter id="Q" symbol="Q" name="Glutamine" colour="008000"/>
+<letter id="R" symbol="R" name="Arginine" colour="CC0000"/>
+<letter id="S" symbol="S" name="Serine" colour="008000"/>
+<letter id="T" symbol="T" name="Threonine" colour="008000"/>
+<letter id="V" symbol="V" name="Valine" colour="0000CC"/>
+<letter id="W" symbol="W" name="Tryptophan" colour="0000CC"/>
+<letter id="Y" symbol="Y" name="Tyrosine" colour="33E6CC"/>
+<letter id="X" symbol="X" aliases="*." equals="ACDEFGHIKLMNPQRSTVWY" name="Any amino acid"/>
+<letter id="B" symbol="B" equals="DN" name="Asparagine or Aspartic acid"/>
+<letter id="Z" symbol="Z" equals="EQ" name="Glutamine or Glutamic acid"/>
+<letter id="J" symbol="J" equals="IL" name="Leucine or Isoleucine"/>
+</alphabet>
+<motif name="1" width="11" best-possible-match="GGGGTATAAAA"/>
+<background source="non-redundant database">
+<value letter="A">0.073</value>
+<value letter="C">0.018</value>
+<value letter="D">0.052</value>
+<value letter="E">0.062</value>
+<value letter="F">0.040</value>
+<value letter="G">0.069</value>
+<value letter="H">0.022</value>
+<value letter="I">0.056</value>
+<value letter="K">0.058</value>
+<value letter="L">0.092</value>
+<value letter="M">0.023</value>
+<value letter="N">0.046</value>
+<value letter="P">0.051</value>
+<value letter="Q">0.041</value>
+<value letter="R">0.052</value>
+<value letter="S">0.074</value>
+<value letter="T">0.059</value>
+<value letter="V">0.064</value>
+<value letter="W">0.013</value>
+<value letter="Y">0.033</value>
+</background>
+<cisml-file>cisml.xml</cisml-file>
+</fimo>

diff -r e416c7c26977 -r d20e391eb22f test-data/phiX.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/phiX.fasta Tue Dec 22 17:02:11 2015 -0500

@@ -0,0 +1,79 @@
+>phiX174
+GAGTTTTATCGCTTCCATGACGCAGAAGTTAACACTTTCGGATATTTCTGATGAGTCGAAAAATTATCTT
+GATAAAGCAGGAATTACTACTGCTTGTTTACGAATTAAATCGAAGTGGACTGCTGGCGGAAAATGAGAAA
+ATTCGACCTATCCTTGCGCAGCTCGAGAAGCTCTTACTTTGCGACCTTTCGCCATCAACTAACGATTCTG
+TCAAAAACTGACGCGTTGGATGAGGAGAAGTGGCTTAATATGCTTGGCACGTTCGTCAAGGACTGGTTTA
+GATATGAGTCACATTTTGTTCATGGTAGAGATTCTCTTGTTGACATTTTAAAAGAGCGTGGATTACTATC
+TGAGTCCGATGCTGTTCAACCACTAATAGGTAAGAAATCATGAGTCAAGTTACTGAACAATCCGTACGTT
+TCCAGACCGCTTTGGCCTCTATTAAGCTCATTCAGGCTTCTGCCGTTTTGGATTTAACCGAAGATGATTT
+CGATTTTCTGACGAGTAACAAAGTTTGGATTGCTACTGACCGCTCTCGTGCTCGTCGCTGCGTTGAGGCT
+TGCGTTTATGGTACGCTGGACTTTGTGGGATACCCTCGCTTTCCTGCTCCTGTTGAGTTTATTGCTGCCG
+TCATTGCTTATTATGTTCATCCCGTCAACATTCAAACGGCCTGTCTCATCATGGAAGGCGCTGAATTTAC
+GGAAAACATTATTAATGGCGTCGAGCGTCCGGTTAAAGCCGCTGAATTGTTCGCGTTTACCTTGCGTGTA
+CGCGCAGGAAACACTGACGTTCTTACTGACGCAGAAGAAAACGTGCGTCAAAAATTACGTGCAGAAGGAG
+TGATGTAATGTCTAAAGGTAAAAAACGTTCTGGCGCTCGCCCTGGTCGTCCGCAGCCGTTGCGAGGTACT
+AAAGGCAAGCGTAAAGGCGCTCGTCTTTGGTATGTAGGTGGTCAACAATTTTAATTGCAGGGGCTTCGGC
+CCCTTACTTGAGGATAAATTATGTCTAATATTCAAACTGGCGCCGAGCGTATGCCGCATGACCTTTCCCA
+TCTTGGCTTCCTTGCTGGTCAGATTGGTCGTCTTATTACCATTTCAACTACTCCGGTTATCGCTGGCGAC
+TCCTTCGAGATGGACGCCGTTGGCGCTCTCCGTCTTTCTCCATTGCGTCGTGGCCTTGCTATTGACTCTA
+CTGTAGACATTTTTACTTTTTATGTCCCTCATCGTCACGTTTATGGTGAACAGTGGATTAAGTTCATGAA
+GGATGGTGTTAATGCCACTCCTCTCCCGACTGTTAACACTACTGGTTATATTGACCATGCCGCTTTTCTT
+GGCACGATTAACCCTGATACCAATAAAATCCCTAAGCATTTGTTTCAGGGTTATTTGAATATCTATAACA
+ACTATTTTAAAGCGCCGTGGATGCCTGACCGTACCGAGGCTAACCCTAATGAGCTTAATCAAGATGATGC
+TCGTTATGGTTTCCGTTGCTGCCATCTCAAAAACATTTGGACTGCTCCGCTTCCTCCTGAGACTGAGCTT
+TCTCGCCAAATGACGACTTCTACCACATCTATTGACATTATGGGTCTGCAAGCTGCTTATGCTAATTTGC
+ATACTGACCAAGAACGTGATTACTTCATGCAGCGTTACCGTGATGTTATTTCTTCATTTGGAGGTAAAAC
+CTCTTATGACGCTGACAACCGTCCTTTACTTGTCATGCGCTCTAATCTCTGGGCATCTGGCTATGATGTT
+GATGGAACTGACCAAACGTCGTTAGGCCAGTTTTCTGGTCGTGTTCAACAGACCTATAAACATTCTGTGC
+CGCGTTTCTTTGTTCCTGAGCATGGCACTATGTTTACTCTTGCGCTTGTTCGTTTTCCGCCTACTGCGAC
+TAAAGAGATTCAGTACCTTAACGCTAAAGGTGCTTTGACTTATACCGATATTGCTGGCGACCCTGTTTTG
+TATGGCAACTTGCCGCCGCGTGAAATTTCTATGAAGGATGTTTTCCGTTCTGGTGATTCGTCTAAGAAGT
+TTAAGATTGCTGAGGGTCAGTGGTATCGTTATGCGCCTTCGTATGTTTCTCCTGCTTATCACCTTCTTGA
+AGGCTTCCCATTCATTCAGGAACCGCCTTCTGGTGATTTGCAAGAACGCGTACTTATTCGCCACCATGAT
+TATGACCAGTGTTTCCAGTCCGTTCAGTTGTTGCAGTGGAATAGTCAGGTTAAATTTAATGTGACCGTTT
+ATCGCAATCTGCCGACCACTCGCGATTCAATCATGACTTCGTGATAAAAGATTGAGTGTGAGGTTATAAC
+GCCGAAGCGGTAAAAATTTTAATTTTTGCCGCTGAGGGGTTGACCAAGCGAAGCGCGGTAGGTTTTCTGC
+TTAGGAGTTTAATCATGTTTCAGACTTTTATTTCTCGCCATAATTCAAACTTTTTTTCTGATAAGCTGGT
+TCTCACTTCTGTTACTCCAGCTTCTTCGGCACCTGTTTTACAGACACCTAAAGCTACATCGTCAACGTTA
+TATTTTGATAGTTTGACGGTTAATGCTGGTAATGGTGGTTTTCTTCATTGCATTCAGATGGATACATCTG
+TCAACGCCGCTAATCAGGTTGTTTCTGTTGGTGCTGATATTGCTTTTGATGCCGACCCTAAATTTTTTGC
+CTGTTTGGTTCGCTTTGAGTCTTCTTCGGTTCCGACTACCCTCCCGACTGCCTATGATGTTTATCCTTTG
+AATGGTCGCCATGATGGTGGTTATTATACCGTCAAGGACTGTGTGACTATTGACGTCCTTCCCCGTACGC
+CGGGCAATAATGTTTATGTTGGTTTCATGGTTTGGTCTAACTTTACCGCTACTAAATGCCGCGGATTGGT
+TTCGCTGAATCAGGTTATTAAAGAGATTATTTGTCTCCAGCCACTTAAGTGAGGTGATTTATGTTTGGTG
+CTATTGCTGGCGGTATTGCTTCTGCTCTTGCTGGTGGCGCCATGTCTAAATTGTTTGGAGGCGGTCAAAA
+AGCCGCCTCCGGTGGCATTCAAGGTGATGTGCTTGCTACCGATAACAATACTGTAGGCATGGGTGATGCT
+GGTATTAAATCTGCCATTCAAGGCTCTAATGTTCCTAACCCTGATGAGGCCGCCCCTAGTTTTGTTTCTG
+GTGCTATGGCTAAAGCTGGTAAAGGACTTCTTGAAGGTACGTTGCAGGCTGGCACTTCTGCCGTTTCTGA
+TAAGTTGCTTGATTTGGTTGGACTTGGTGGCAAGTCTGCCGCTGATAAAGGAAAGGATACTCGTGATTAT
+CTTGCTGCTGCATTTCCTGAGCTTAATGCTTGGGAGCGTGCTGGTGCTGATGCTTCCTCTGCTGGTATGG
+TTGACGCCGGATTTGAGAATCAAAAAGAGCTTACTAAAATGCAACTGGACAATCAGAAAGAGATTGCCGA
+GATGCAAAATGAGACTCAAAAAGAGATTGCTGGCATTCAGTCGGCGACTTCACGCCAGAATACGAAAGAC
+CAGGTATATGCACAAAATGAGATGCTTGCTTATCAACAGAAGGAGTCTACTGCTCGCGTTGCGTCTATTA
+TGGAAAACACCAATCTTTCCAAGCAACAGCAGGTTTCCGAGATTATGCGCCAAATGCTTACTCAAGCTCA
+AACGGCTGGTCAGTATTTTACCAATGACCAAATCAAAGAAATGACTCGCAAGGTTAGTGCTGAGGTTGAC
+TTAGTTCATCAGCAAACGCAGAATCAGCGGTATGGCTCTTCTCATATTGGCGCTACTGCAAAGGATATTT
+CTAATGTCGTCACTGATGCTGCTTCTGGTGTGGTTGATATTTTTCATGGTATTGATAAAGCTGTTGCCGA
+TACTTGGAACAATTTCTGGAAAGACGGTAAAGCTGATGGTATTGGCTCTAATTTGTCTAGGAAATAACCG
+TCAGGATTGACACCCTCCCAATTGTATGTTTTCATGCCTCCAAATCTTGGAGGCTTTTTTATGGTTCGTT
+CTTATTACCCTTCTGAATGTCACGCTGATTATTTTGACTTTGAGCGTATCGAGGCTCTTAAACCTGCTAT
+TGAGGCTTGTGGCATTTCTACTCTTTCTCAATCCCCAATGCTTGGCTTCCATAAGCAGATGGATAACCGC
+ATCAAGCTCTTGGAAGAGATTCTGTCTTTTCGTATGCAGGGCGTTGAGTTCGATAATGGTGATATGTATG
+TTGACGGCCATAAGGCTGCTTCTGACGTTCGTGATGAGTTTGTATCTGTTACTGAGAAGTTAATGGATGA
+ATTGGCACAATGCTACAATGTGCTCCCCCAACTTGATATTAATAACACTATAGACCACCGCCCCGAAGGG
+GACGAAAAATGGTTTTTAGAGAACGAGAAGACGGTTACGCAGTTTTGCCGCAAGCTGGCTGCTGAACGCC
+CTCTTAAGGATATTCGCGATGAGTATAATTACCCCAAAAAGAAAGGTATTAAGGATGAGTGTTCAAGATT
+GCTGGAGGCCTCCACTATGAAATCGCGTAGAGGCTTTACTATTCAGCGTTTGATGAATGCAATGCGACAG
+GCTCATGCTGATGGTTGGTTTATCGTTTTTGACACTCTCACGTTGGCTGACGACCGATTAGAGGCGTTTT
+ATGATAATCCCAATGCTTTGCGTGACTATTTTCGTGATATTGGTCGTATGGTTCTTGCTGCCGAGGGTCG
+CAAGGCTAATGATTCACACGCCGACTGCTATCAGTATTTTTGTGTGCCTGAGTATGGTACAGCTAATGGC
+CGTCTTCATTTCCATGCGGTGCATTTTATGCGGACACTTCCTACAGGTAGCGTTGACCCTAATTTTGGTC
+GTCGGGTACGCAATCGCCGCCAGTTAAATAGCTTGCAAAATACGTGGCCTTATGGTTACAGTATGCCCAT
+CGCAGTTCGCTACACGCAGGACGCTTTTTCACGTTCTGGTTGGTTGTGGCCTGTTGATGCTAAAGGTGAG
+CCGCTTAAAGCTACCAGTTATATGGCTGTTGGTTTCTATGTGGCTAAATACGTTAACAAAAAGTCAGATA
+TGGACCTTGCTGCTAAAGGTCTAGGAGCTAAAGAATGGAACAACTCACTAAAAACCAAGCTGTCGCTACT
+TCCCAAGAAGCTGTTCAGAATCAGAATGAGCCGCAACTTCGGGATGAAAATGCTCACAATGACAAATCTG
+TCCACGGAGTGCTTAATCCAACTTACCAAGCTGGGTTACGACGCGACGCCGTTCAACCAGATATTGAAGC
+AGAACGCAAAAAGAGAGATGAGATTGAGGCTGGGAAAAGTTACTGTAGCCGACGTTTTGGCGGCGCAACC
+TGTGACGACAAATCTGCTCAAATTTATGCGCGCTTCGATAAAAATGATTGGCGTATCCAACCTGCA
+

diff -r e416c7c26977 -r d20e391eb22f tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Tue Dec 22 17:02:11 2015 -0500

@@ -0,0 +1,7 @@
+<tables>
+    
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>