# HG changeset patch
# User iuc
# Date 1466183812 14400
# Node ID 62d1fae3b7d30a44e31c0e7847089aea5a2eaf31
# Parent  34c794383f815687265fec3afe2f39ab2969e7f8
Uploaded

diff -r 34c794383f81 -r 62d1fae3b7d3 fimo_wrapper.py
--- a/fimo_wrapper.py	Fri Mar 18 08:23:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,134 +0,0 @@
-#!/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 34c794383f81 -r 62d1fae3b7d3 test-data/fimo_output_almost-gff_1.txt
--- a/test-data/fimo_output_almost-gff_1.txt	Fri Mar 18 08:23:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-##gff-version 3
-phiX174	fimo	polypeptide_motif	1388	1398	102	+	.	Name=1;ID=1-1-phiX174;pvalue=6.36e-11;qvalue= 1.25e-09;sequence=AATATCTATAA;
-phiX174	fimo	polypeptide_motif	847	857	102	+	.	Name=1;ID=1-2-phiX174;pvalue=7.02e-11;qvalue= 1.25e-09;sequence=AATGTCTAAAG;
-phiX174	fimo	polypeptide_motif	2301	2311	99.6	+	.	Name=1;ID=1-3-phiX174;pvalue=1.08e-10;qvalue= 1.29e-09;sequence=AGGTTATAACG;
-phiX174	fimo	polypeptide_motif	5063	5073	95.6	+	.	Name=1;ID=1-4-phiX174;pvalue=2.73e-10;qvalue= 2.25e-09;sequence=AGGAGCTAAAG;
-phiX174	fimo	polypeptide_motif	989	999	 95	+	.	Name=1;ID=1-5-phiX174;pvalue=3.15e-10;qvalue= 2.25e-09;sequence=TGAGGATAAAT;
-phiX174	fimo	polypeptide_motif	4713	4723	91.1	+	.	Name=1;ID=1-6-phiX174;pvalue=7.74e-10;qvalue= 3.48e-09;sequence=GACTGCTATCA;
-phiX174	fimo	polypeptide_motif	5048	5058	90.7	+	.	Name=1;ID=1-7-phiX174;pvalue=8.51e-10;qvalue= 3.48e-09;sequence=TGCTGCTAAAG;
-phiX174	fimo	polypeptide_motif	855	865	90.6	+	.	Name=1;ID=1-8-phiX174;pvalue=8.64e-10;qvalue= 3.48e-09;sequence=AAGGTAAAAAA;
-phiX174	fimo	polypeptide_motif	3155	3165	90.1	+	.	Name=1;ID=1-9-phiX174;pvalue=9.76e-10;qvalue= 3.48e-09;sequence=TATGGCTAAAG;
-phiX174	fimo	polypeptide_motif	5009	5019	90.1	+	.	Name=1;ID=1-10-phiX174;pvalue=9.76e-10;qvalue= 3.48e-09;sequence=TGTGGCTAAAT;
-phiX174	fimo	polypeptide_motif	814	824	88.9	+	.	Name=1;ID=1-11-phiX174;pvalue=1.28e-09;qvalue= 4.14e-09;sequence=TGCGTCAAAAA;
-phiX174	fimo	polypeptide_motif	2832	2842	88.5	+	.	Name=1;ID=1-12-phiX174;pvalue=1.42e-09;qvalue= 4.23e-09;sequence=TTGGTCTAACT;
-phiX174	fimo	polypeptide_motif	3830	3840	87.7	+	.	Name=1;ID=1-13-phiX174;pvalue=1.7e-09;qvalue= 4.68e-09;sequence=TATTGATAAAG;
-phiX174	fimo	polypeptide_motif	3560	3570	87.2	+	.	Name=1;ID=1-14-phiX174;pvalue=1.89e-09;qvalue= 4.82e-09;sequence=TGCGTCTATTA;
-phiX174	fimo	polypeptide_motif	2882	2892	86.4	+	.	Name=1;ID=1-15-phiX174;pvalue=2.29e-09;qvalue= 5.46e-09;sequence=AGGTTATTAAA;
-phiX174	fimo	polypeptide_motif	4453	4463	85.9	+	.	Name=1;ID=1-16-phiX174;pvalue=2.58e-09;qvalue= 5.75e-09;sequence=AAGGTATTAAG;
-phiX174	fimo	polypeptide_motif	2493	2503	85.1	+	.	Name=1;ID=1-17-phiX174;pvalue=3.06e-09;qvalue= 5.79e-09;sequence=GACACCTAAAG;
-phiX174	fimo	polypeptide_motif	4104	4114	85.1	+	.	Name=1;ID=1-18-phiX174;pvalue=3.08e-09;qvalue= 5.79e-09;sequence=GGCTTCCATAA;
-phiX174	fimo	polypeptide_motif	4955	4965	85.1	+	.	Name=1;ID=1-19-phiX174;pvalue=3.08e-09;qvalue= 5.79e-09;sequence=TGATGCTAAAG;
-phiX174	fimo	polypeptide_motif	1885	1895	84.4	+	.	Name=1;ID=1-20-phiX174;pvalue=3.61e-09;qvalue= 6.45e-09;sequence=TGCGACTAAAG;
-phiX174	fimo	polypeptide_motif	3376	3386	84.2	+	.	Name=1;ID=1-21-phiX174;pvalue=3.81e-09;qvalue= 6.48e-09;sequence=AGAATCAAAAA;
-phiX174	fimo	polypeptide_motif	52	62	83.9	+	.	Name=1;ID=1-22-phiX174;pvalue=4.06e-09;qvalue= 6.58e-09;sequence=TGAGTCGAAAA;
-phiX174	fimo	polypeptide_motif	1390	1400	83.7	+	.	Name=1;ID=1-23-phiX174;pvalue=4.26e-09;qvalue= 6.61e-09;sequence=TATCTATAACA;
-phiX174	fimo	polypeptide_motif	2017	2027	83.4	+	.	Name=1;ID=1-24-phiX174;pvalue=4.6e-09;qvalue= 6.85e-09;sequence=TTCGTCTAAGA;
-phiX174	fimo	polypeptide_motif	1000	1010	83.1	+	.	Name=1;ID=1-25-phiX174;pvalue=4.88e-09;qvalue= 6.97e-09;sequence=TATGTCTAATA;
-phiX174	fimo	polypeptide_motif	1555	1565	82.5	+	.	Name=1;ID=1-26-phiX174;pvalue=5.58e-09;qvalue= 7.37e-09;sequence=GACTTCTACCA;
-phiX174	fimo	polypeptide_motif	4430	4440	82.5	+	.	Name=1;ID=1-27-phiX174;pvalue=5.62e-09;qvalue= 7.37e-09;sequence=TGAGTATAATT;
-phiX174	fimo	polypeptide_motif	1927	1937	82.3	+	.	Name=1;ID=1-28-phiX174;pvalue=5.82e-09;qvalue= 7.37e-09;sequence=GACTTATACCG;
-phiX174	fimo	polypeptide_motif	2981	2991	82.1	+	.	Name=1;ID=1-29-phiX174;pvalue=6.13e-09;qvalue= 7.37e-09;sequence=CATGTCTAAAT;
-phiX174	fimo	polypeptide_motif	4203	4213	 82	+	.	Name=1;ID=1-30-phiX174;pvalue=6.34e-09;qvalue= 7.37e-09;sequence=GACGGCCATAA;
-phiX174	fimo	polypeptide_motif	1669	1679	81.9	+	.	Name=1;ID=1-31-phiX174;pvalue=6.4e-09;qvalue= 7.37e-09;sequence=TGGAGGTAAAA;
-phiX174	fimo	polypeptide_motif	3260	3270	81.5	+	.	Name=1;ID=1-32-phiX174;pvalue=7.01e-09;qvalue= 7.82e-09;sequence=CGCTGATAAAG;
-phiX174	fimo	polypeptide_motif	3047	3057	81.3	+	.	Name=1;ID=1-33-phiX174;pvalue=7.4e-09;qvalue= 7.85e-09;sequence=TACCGATAACA;
-phiX174	fimo	polypeptide_motif	4176	4186	81.2	+	.	Name=1;ID=1-34-phiX174;pvalue=7.6e-09;qvalue= 7.85e-09;sequence=GAGTTCGATAA;
-phiX174	fimo	polypeptide_motif	4118	4128	81.1	+	.	Name=1;ID=1-35-phiX174;pvalue=7.7e-09;qvalue= 7.85e-09;sequence=GATGGATAACC;
-phiX174	fimo	polypeptide_motif	5370	5380	80.9	+	.	Name=1;ID=1-36-phiX174;pvalue=8.03e-09;qvalue= 7.87e-09;sequence=GGCGTATCCAA;
-phiX174	fimo	polypeptide_motif	1242	1252	80.5	+	.	Name=1;ID=1-37-phiX174;pvalue=8.94e-09;qvalue= 7.87e-09;sequence=AGTGGATTAAG;
-phiX174	fimo	polypeptide_motif	2583	2593	80.5	+	.	Name=1;ID=1-38-phiX174;pvalue=8.94e-09;qvalue= 7.87e-09;sequence=TACATCTGTCA;
-phiX174	fimo	polypeptide_motif	698	708	80.4	+	.	Name=1;ID=1-39-phiX174;pvalue=9.13e-09;qvalue= 7.87e-09;sequence=TACGGAAAACA;
-phiX174	fimo	polypeptide_motif	2299	2309	80.3	+	.	Name=1;ID=1-40-phiX174;pvalue=9.26e-09;qvalue= 7.87e-09;sequence=TGAGGTTATAA;
-phiX174	fimo	polypeptide_motif	4189	4199	80.1	+	.	Name=1;ID=1-41-phiX174;pvalue=9.69e-09;qvalue= 7.87e-09;sequence=GTGATATGTAT;
-phiX174	fimo	polypeptide_motif	275	285	80.1	+	.	Name=1;ID=1-42-phiX174;pvalue=9.85e-09;qvalue= 7.87e-09;sequence=GGTTTAGATAT;
-phiX174	fimo	polypeptide_motif	1801	1811	 80	+	.	Name=1;ID=1-43-phiX174;pvalue=1e-08;qvalue= 7.87e-09;sequence=GACCTATAAAC;
-phiX174	fimo	polypeptide_motif	1386	1396	79.9	+	.	Name=1;ID=1-44-phiX174;pvalue=1.03e-08;qvalue= 7.87e-09;sequence=TGAATATCTAT;
-phiX174	fimo	polypeptide_motif	1303	1313	79.8	+	.	Name=1;ID=1-45-phiX174;pvalue=1.03e-08;qvalue= 7.87e-09;sequence=TGGTTATATTG;
-phiX174	fimo	polypeptide_motif	3772	3782	79.8	+	.	Name=1;ID=1-46-phiX174;pvalue=1.04e-08;qvalue= 7.87e-09;sequence=AGGATATTTCT;
-phiX174	fimo	polypeptide_motif	1288	1298	79.8	+	.	Name=1;ID=1-47-phiX174;pvalue=1.04e-08;qvalue= 7.87e-09;sequence=GACTGTTAACA;
-phiX174	fimo	polypeptide_motif	2577	2587	79.7	+	.	Name=1;ID=1-48-phiX174;pvalue=1.08e-08;qvalue= 7.87e-09;sequence=GATGGATACAT;
-phiX174	fimo	polypeptide_motif	937	947	79.6	+	.	Name=1;ID=1-49-phiX174;pvalue=1.08e-08;qvalue= 7.87e-09;sequence=TTGGTATGTAG;
-phiX174	fimo	polypeptide_motif	904	914	79.5	+	.	Name=1;ID=1-50-phiX174;pvalue=1.11e-08;qvalue= 7.93e-09;sequence=AGGTACTAAAG;
-phiX174	fimo	polypeptide_motif	2279	2289	79.4	+	.	Name=1;ID=1-51-phiX174;pvalue=1.13e-08;qvalue= 7.93e-09;sequence=TCGTGATAAAA;
-phiX174	fimo	polypeptide_motif	3164	3174	79.3	+	.	Name=1;ID=1-52-phiX174;pvalue=1.16e-08;qvalue= 7.98e-09;sequence=AGCTGGTAAAG;
-phiX174	fimo	polypeptide_motif	24	34	79.1	+	.	Name=1;ID=1-53-phiX174;pvalue=1.23e-08;qvalue= 8.24e-09;sequence=AGAAGTTAACA;
-phiX174	fimo	polypeptide_motif	838	848	78.9	+	.	Name=1;ID=1-54-phiX174;pvalue=1.27e-08;qvalue= 8.24e-09;sequence=GAGTGATGTAA;
-phiX174	fimo	polypeptide_motif	853	863	78.9	+	.	Name=1;ID=1-55-phiX174;pvalue=1.27e-08;qvalue= 8.24e-09;sequence=TAAAGGTAAAA;
-phiX174	fimo	polypeptide_motif	1984	1994	78.6	+	.	Name=1;ID=1-56-phiX174;pvalue=1.36e-08;qvalue= 8.68e-09;sequence=AATTTCTATGA;
-phiX174	fimo	polypeptide_motif	1	11	78.3	+	.	Name=1;ID=1-57-phiX174;pvalue=1.46e-08;qvalue= 9.05e-09;sequence=GAGTTTTATCG;
-phiX174	fimo	polypeptide_motif	4307	4317	78.3	+	.	Name=1;ID=1-58-phiX174;pvalue=1.47e-08;qvalue= 9.05e-09;sequence=TATTAATAACA;
-phiX174	fimo	polypeptide_motif	4303	4313	78.2	+	.	Name=1;ID=1-59-phiX174;pvalue=1.52e-08;qvalue= 9.19e-09;sequence=TTGATATTAAT;
-phiX174	fimo	polypeptide_motif	5033	5043	 78	+	.	Name=1;ID=1-60-phiX174;pvalue=1.58e-08;qvalue= 9.41e-09;sequence=GTCAGATATGG;
-phiX174	fimo	polypeptide_motif	2579	2589	77.6	+	.	Name=1;ID=1-61-phiX174;pvalue=1.73e-08;qvalue= 1.01e-08;sequence=TGGATACATCT;
-phiX174	fimo	polypeptide_motif	322	332	77.4	+	.	Name=1;ID=1-62-phiX174;pvalue=1.82e-08;qvalue= 1.05e-08;sequence=GACATTTTAAA;
-phiX174	fimo	polypeptide_motif	5001	5011	76.8	+	.	Name=1;ID=1-63-phiX174;pvalue=2.09e-08;qvalue= 1.19e-08;sequence=GGTTTCTATGT;
-phiX174	fimo	polypeptide_motif	4217	4227	76.7	+	.	Name=1;ID=1-64-phiX174;pvalue=2.15e-08;qvalue= 1.2e-08;sequence=TGCTTCTGACG;
-phiX174	fimo	polypeptide_motif	4262	4272	76.6	+	.	Name=1;ID=1-65-phiX174;pvalue=2.18e-08;qvalue= 1.2e-08;sequence=AATGGATGAAT;
-phiX174	fimo	polypeptide_motif	3569	3579	76.5	+	.	Name=1;ID=1-66-phiX174;pvalue=2.26e-08;qvalue= 1.22e-08;sequence=TATGGAAAACA;
-phiX174	fimo	polypeptide_motif	194	204	76.4	+	.	Name=1;ID=1-67-phiX174;pvalue=2.29e-08;qvalue= 1.22e-08;sequence=ATCAACTAACG;
-phiX174	fimo	polypeptide_motif	131	141	 76	+	.	Name=1;ID=1-68-phiX174;pvalue=2.49e-08;qvalue= 1.31e-08;sequence=AAATGAGAAAA;
-phiX174	fimo	polypeptide_motif	1491	1501	75.9	+	.	Name=1;ID=1-69-phiX174;pvalue=2.55e-08;qvalue= 1.32e-08;sequence=GCCATCTCAAA;
-phiX174	fimo	polypeptide_motif	434	444	75.7	+	.	Name=1;ID=1-70-phiX174;pvalue=2.67e-08;qvalue= 1.36e-08;sequence=GGCCTCTATTA;
-phiX174	fimo	polypeptide_motif	4565	4575	75.6	+	.	Name=1;ID=1-71-phiX174;pvalue=2.73e-08;qvalue= 1.36e-08;sequence=TTGGTTTATCG;
-phiX174	fimo	polypeptide_motif	102	112	75.6	+	.	Name=1;ID=1-72-phiX174;pvalue=2.75e-08;qvalue= 1.36e-08;sequence=GAATTAAATCG;
-phiX174	fimo	polypeptide_motif	903	913	75.5	+	.	Name=1;ID=1-73-phiX174;pvalue=2.82e-08;qvalue= 1.38e-08;sequence=GAGGTACTAAA;
-phiX174	fimo	polypeptide_motif	4748	4758	75.2	+	.	Name=1;ID=1-74-phiX174;pvalue=3.01e-08;qvalue= 1.45e-08;sequence=TACAGCTAATG;
-phiX174	fimo	polypeptide_motif	2622	2632	 75	+	.	Name=1;ID=1-75-phiX174;pvalue=3.16e-08;qvalue= 1.5e-08;sequence=TGCTGATATTG;
-phiX174	fimo	polypeptide_motif	467	477	74.7	+	.	Name=1;ID=1-76-phiX174;pvalue=3.35e-08;qvalue= 1.57e-08;sequence=TTTGGATTTAA;
-phiX174	fimo	polypeptide_motif	4033	4043	74.6	+	.	Name=1;ID=1-77-phiX174;pvalue=3.44e-08;qvalue= 1.58e-08;sequence=AGCGTATCGAG;
-phiX174	fimo	polypeptide_motif	1348	1358	74.6	+	.	Name=1;ID=1-78-phiX174;pvalue=3.46e-08;qvalue= 1.58e-08;sequence=TACCAATAAAA;
-phiX174	fimo	polypeptide_motif	239	249	74.4	+	.	Name=1;ID=1-79-phiX174;pvalue=3.62e-08;qvalue= 1.64e-08;sequence=AGTGGCTTAAT;
-phiX174	fimo	polypeptide_motif	500	510	74.1	+	.	Name=1;ID=1-80-phiX174;pvalue=3.84e-08;qvalue= 1.71e-08;sequence=GACGAGTAACA;
-phiX174	fimo	polypeptide_motif	3001	3011	 74	+	.	Name=1;ID=1-81-phiX174;pvalue=3.93e-08;qvalue= 1.73e-08;sequence=GCGGTCAAAAA;
-phiX174	fimo	polypeptide_motif	3776	3786	 74	+	.	Name=1;ID=1-82-phiX174;pvalue=3.98e-08;qvalue= 1.73e-08;sequence=TATTTCTAATG;
-phiX174	fimo	polypeptide_motif	2026	2036	73.9	+	.	Name=1;ID=1-83-phiX174;pvalue=4.06e-08;qvalue= 1.75e-08;sequence=GAAGTTTAAGA;
-phiX174	fimo	polypeptide_motif	4237	4247	73.8	+	.	Name=1;ID=1-84-phiX174;pvalue=4.12e-08;qvalue= 1.75e-08;sequence=AGTTTGTATCT;
-phiX174	fimo	polypeptide_motif	803	813	73.7	+	.	Name=1;ID=1-85-phiX174;pvalue=4.24e-08;qvalue= 1.78e-08;sequence=AGAAGAAAACG;
-phiX174	fimo	polypeptide_motif	3770	3780	73.6	+	.	Name=1;ID=1-86-phiX174;pvalue=4.35e-08;qvalue= 1.81e-08;sequence=AAAGGATATTT;
-phiX174	fimo	polypeptide_motif	3429	3439	73.5	+	.	Name=1;ID=1-87-phiX174;pvalue=4.45e-08;qvalue= 1.82e-08;sequence=GAGATGCAAAA;
-phiX174	fimo	polypeptide_motif	99	109	73.5	+	.	Name=1;ID=1-88-phiX174;pvalue=4.48e-08;qvalue= 1.82e-08;sequence=TACGAATTAAA;
-phiX174	fimo	polypeptide_motif	67	77	73.2	+	.	Name=1;ID=1-89-phiX174;pvalue=4.78e-08;qvalue= 1.92e-08;sequence=TCTTGATAAAG;
-phiX174	fimo	polypeptide_motif	5332	5342	72.9	+	.	Name=1;ID=1-90-phiX174;pvalue=5.13e-08;qvalue= 2.01e-08;sequence=ATCTGCTCAAA;
-phiX174	fimo	polypeptide_motif	277	287	72.9	+	.	Name=1;ID=1-91-phiX174;pvalue=5.14e-08;qvalue= 2.01e-08;sequence=TTTAGATATGA;
-phiX174	fimo	polypeptide_motif	4338	4348	72.8	+	.	Name=1;ID=1-92-phiX174;pvalue=5.18e-08;qvalue= 2.01e-08;sequence=GGGGACGAAAA;
-phiX174	fimo	polypeptide_motif	3812	3822	72.8	+	.	Name=1;ID=1-93-phiX174;pvalue=5.28e-08;qvalue= 2.03e-08;sequence=GGTTGATATTT;
-phiX174	fimo	polypeptide_motif	1909	1919	72.6	+	.	Name=1;ID=1-94-phiX174;pvalue=5.51e-08;qvalue= 2.08e-08;sequence=TAACGCTAAAG;
-phiX174	fimo	polypeptide_motif	3000	3010	72.6	+	.	Name=1;ID=1-95-phiX174;pvalue=5.54e-08;qvalue= 2.08e-08;sequence=GGCGGTCAAAA;
-phiX174	fimo	polypeptide_motif	3891	3901	72.4	+	.	Name=1;ID=1-96-phiX174;pvalue=5.75e-08;qvalue= 2.11e-08;sequence=ATTGGCTCTAA;
-phiX174	fimo	polypeptide_motif	3079	3089	72.4	+	.	Name=1;ID=1-97-phiX174;pvalue=5.76e-08;qvalue= 2.11e-08;sequence=CTGGTATTAAA;
-phiX174	fimo	polypeptide_motif	37	47	72.4	+	.	Name=1;ID=1-98-phiX174;pvalue=5.79e-08;qvalue= 2.11e-08;sequence=TTCGGATATTT;
-phiX174	fimo	polypeptide_motif	380	390	72.2	+	.	Name=1;ID=1-99-phiX174;pvalue=6.01e-08;qvalue= 2.17e-08;sequence=GTAAGAAATCA;
diff -r 34c794383f81 -r 62d1fae3b7d3 test-data/fimo_output_almost-gff_2.txt
--- a/test-data/fimo_output_almost-gff_2.txt	Fri Mar 18 08:23:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-##gff-version 3
-phiX174	fimo	polypeptide_motif	1388	1398	102	+	.	Name=1;ID=1-1-phiX174;pvalue=6.36e-11;sequence=AATATCTATAA;
-phiX174	fimo	polypeptide_motif	847	857	102	+	.	Name=1;ID=1-2-phiX174;pvalue=7.02e-11;sequence=AATGTCTAAAG;
-phiX174	fimo	polypeptide_motif	2301	2311	99.6	+	.	Name=1;ID=1-3-phiX174;pvalue=1.08e-10;sequence=AGGTTATAACG;
-phiX174	fimo	polypeptide_motif	5063	5073	95.6	+	.	Name=1;ID=1-4-phiX174;pvalue=2.73e-10;sequence=AGGAGCTAAAG;
-phiX174	fimo	polypeptide_motif	989	999	 95	+	.	Name=1;ID=1-5-phiX174;pvalue=3.15e-10;sequence=TGAGGATAAAT;
-phiX174	fimo	polypeptide_motif	4713	4723	91.1	+	.	Name=1;ID=1-6-phiX174;pvalue=7.74e-10;sequence=GACTGCTATCA;
-phiX174	fimo	polypeptide_motif	5048	5058	90.7	+	.	Name=1;ID=1-7-phiX174;pvalue=8.51e-10;sequence=TGCTGCTAAAG;
-phiX174	fimo	polypeptide_motif	855	865	90.6	+	.	Name=1;ID=1-8-phiX174;pvalue=8.64e-10;sequence=AAGGTAAAAAA;
-phiX174	fimo	polypeptide_motif	3155	3165	90.1	+	.	Name=1;ID=1-9-phiX174;pvalue=9.76e-10;sequence=TATGGCTAAAG;
-phiX174	fimo	polypeptide_motif	5009	5019	90.1	+	.	Name=1;ID=1-10-phiX174;pvalue=9.76e-10;sequence=TGTGGCTAAAT;
-phiX174	fimo	polypeptide_motif	814	824	88.9	+	.	Name=1;ID=1-11-phiX174;pvalue=1.28e-09;sequence=TGCGTCAAAAA;
-phiX174	fimo	polypeptide_motif	2832	2842	88.5	+	.	Name=1;ID=1-12-phiX174;pvalue=1.42e-09;sequence=TTGGTCTAACT;
-phiX174	fimo	polypeptide_motif	3830	3840	87.7	+	.	Name=1;ID=1-13-phiX174;pvalue=1.7e-09;sequence=TATTGATAAAG;
-phiX174	fimo	polypeptide_motif	3560	3570	87.2	+	.	Name=1;ID=1-14-phiX174;pvalue=1.89e-09;sequence=TGCGTCTATTA;
-phiX174	fimo	polypeptide_motif	2882	2892	86.4	+	.	Name=1;ID=1-15-phiX174;pvalue=2.29e-09;sequence=AGGTTATTAAA;
-phiX174	fimo	polypeptide_motif	4453	4463	85.9	+	.	Name=1;ID=1-16-phiX174;pvalue=2.58e-09;sequence=AAGGTATTAAG;
-phiX174	fimo	polypeptide_motif	2493	2503	85.1	+	.	Name=1;ID=1-17-phiX174;pvalue=3.06e-09;sequence=GACACCTAAAG;
-phiX174	fimo	polypeptide_motif	4104	4114	85.1	+	.	Name=1;ID=1-18-phiX174;pvalue=3.08e-09;sequence=GGCTTCCATAA;
-phiX174	fimo	polypeptide_motif	4955	4965	85.1	+	.	Name=1;ID=1-19-phiX174;pvalue=3.08e-09;sequence=TGATGCTAAAG;
-phiX174	fimo	polypeptide_motif	1885	1895	84.4	+	.	Name=1;ID=1-20-phiX174;pvalue=3.61e-09;sequence=TGCGACTAAAG;
-phiX174	fimo	polypeptide_motif	3376	3386	84.2	+	.	Name=1;ID=1-21-phiX174;pvalue=3.81e-09;sequence=AGAATCAAAAA;
-phiX174	fimo	polypeptide_motif	52	62	83.9	+	.	Name=1;ID=1-22-phiX174;pvalue=4.06e-09;sequence=TGAGTCGAAAA;
-phiX174	fimo	polypeptide_motif	1390	1400	83.7	+	.	Name=1;ID=1-23-phiX174;pvalue=4.26e-09;sequence=TATCTATAACA;
-phiX174	fimo	polypeptide_motif	2017	2027	83.4	+	.	Name=1;ID=1-24-phiX174;pvalue=4.6e-09;sequence=TTCGTCTAAGA;
-phiX174	fimo	polypeptide_motif	1000	1010	83.1	+	.	Name=1;ID=1-25-phiX174;pvalue=4.88e-09;sequence=TATGTCTAATA;
-phiX174	fimo	polypeptide_motif	1555	1565	82.5	+	.	Name=1;ID=1-26-phiX174;pvalue=5.58e-09;sequence=GACTTCTACCA;
-phiX174	fimo	polypeptide_motif	4430	4440	82.5	+	.	Name=1;ID=1-27-phiX174;pvalue=5.62e-09;sequence=TGAGTATAATT;
-phiX174	fimo	polypeptide_motif	1927	1937	82.3	+	.	Name=1;ID=1-28-phiX174;pvalue=5.82e-09;sequence=GACTTATACCG;
-phiX174	fimo	polypeptide_motif	2981	2991	82.1	+	.	Name=1;ID=1-29-phiX174;pvalue=6.13e-09;sequence=CATGTCTAAAT;
-phiX174	fimo	polypeptide_motif	4203	4213	 82	+	.	Name=1;ID=1-30-phiX174;pvalue=6.34e-09;sequence=GACGGCCATAA;
-phiX174	fimo	polypeptide_motif	1669	1679	81.9	+	.	Name=1;ID=1-31-phiX174;pvalue=6.4e-09;sequence=TGGAGGTAAAA;
-phiX174	fimo	polypeptide_motif	3260	3270	81.5	+	.	Name=1;ID=1-32-phiX174;pvalue=7.01e-09;sequence=CGCTGATAAAG;
-phiX174	fimo	polypeptide_motif	3047	3057	81.3	+	.	Name=1;ID=1-33-phiX174;pvalue=7.4e-09;sequence=TACCGATAACA;
-phiX174	fimo	polypeptide_motif	4176	4186	81.2	+	.	Name=1;ID=1-34-phiX174;pvalue=7.6e-09;sequence=GAGTTCGATAA;
-phiX174	fimo	polypeptide_motif	4118	4128	81.1	+	.	Name=1;ID=1-35-phiX174;pvalue=7.7e-09;sequence=GATGGATAACC;
-phiX174	fimo	polypeptide_motif	5370	5380	80.9	+	.	Name=1;ID=1-36-phiX174;pvalue=8.03e-09;sequence=GGCGTATCCAA;
-phiX174	fimo	polypeptide_motif	1242	1252	80.5	+	.	Name=1;ID=1-37-phiX174;pvalue=8.94e-09;sequence=AGTGGATTAAG;
-phiX174	fimo	polypeptide_motif	2583	2593	80.5	+	.	Name=1;ID=1-38-phiX174;pvalue=8.94e-09;sequence=TACATCTGTCA;
-phiX174	fimo	polypeptide_motif	698	708	80.4	+	.	Name=1;ID=1-39-phiX174;pvalue=9.13e-09;sequence=TACGGAAAACA;
-phiX174	fimo	polypeptide_motif	2299	2309	80.3	+	.	Name=1;ID=1-40-phiX174;pvalue=9.26e-09;sequence=TGAGGTTATAA;
-phiX174	fimo	polypeptide_motif	4189	4199	80.1	+	.	Name=1;ID=1-41-phiX174;pvalue=9.69e-09;sequence=GTGATATGTAT;
-phiX174	fimo	polypeptide_motif	275	285	80.1	+	.	Name=1;ID=1-42-phiX174;pvalue=9.85e-09;sequence=GGTTTAGATAT;
-phiX174	fimo	polypeptide_motif	1801	1811	 80	+	.	Name=1;ID=1-43-phiX174;pvalue=1e-08;sequence=GACCTATAAAC;
-phiX174	fimo	polypeptide_motif	1386	1396	79.9	+	.	Name=1;ID=1-44-phiX174;pvalue=1.03e-08;sequence=TGAATATCTAT;
-phiX174	fimo	polypeptide_motif	1303	1313	79.8	+	.	Name=1;ID=1-45-phiX174;pvalue=1.03e-08;sequence=TGGTTATATTG;
-phiX174	fimo	polypeptide_motif	3772	3782	79.8	+	.	Name=1;ID=1-46-phiX174;pvalue=1.04e-08;sequence=AGGATATTTCT;
-phiX174	fimo	polypeptide_motif	1288	1298	79.8	+	.	Name=1;ID=1-47-phiX174;pvalue=1.04e-08;sequence=GACTGTTAACA;
-phiX174	fimo	polypeptide_motif	2577	2587	79.7	+	.	Name=1;ID=1-48-phiX174;pvalue=1.08e-08;sequence=GATGGATACAT;
-phiX174	fimo	polypeptide_motif	937	947	79.6	+	.	Name=1;ID=1-49-phiX174;pvalue=1.08e-08;sequence=TTGGTATGTAG;
-phiX174	fimo	polypeptide_motif	904	914	79.5	+	.	Name=1;ID=1-50-phiX174;pvalue=1.11e-08;sequence=AGGTACTAAAG;
-phiX174	fimo	polypeptide_motif	2279	2289	79.4	+	.	Name=1;ID=1-51-phiX174;pvalue=1.13e-08;sequence=TCGTGATAAAA;
-phiX174	fimo	polypeptide_motif	3164	3174	79.3	+	.	Name=1;ID=1-52-phiX174;pvalue=1.16e-08;sequence=AGCTGGTAAAG;
-phiX174	fimo	polypeptide_motif	24	34	79.1	+	.	Name=1;ID=1-53-phiX174;pvalue=1.23e-08;sequence=AGAAGTTAACA;
-phiX174	fimo	polypeptide_motif	838	848	78.9	+	.	Name=1;ID=1-54-phiX174;pvalue=1.27e-08;sequence=GAGTGATGTAA;
-phiX174	fimo	polypeptide_motif	853	863	78.9	+	.	Name=1;ID=1-55-phiX174;pvalue=1.27e-08;sequence=TAAAGGTAAAA;
-phiX174	fimo	polypeptide_motif	1984	1994	78.6	+	.	Name=1;ID=1-56-phiX174;pvalue=1.36e-08;sequence=AATTTCTATGA;
-phiX174	fimo	polypeptide_motif	1	11	78.3	+	.	Name=1;ID=1-57-phiX174;pvalue=1.46e-08;sequence=GAGTTTTATCG;
-phiX174	fimo	polypeptide_motif	4307	4317	78.3	+	.	Name=1;ID=1-58-phiX174;pvalue=1.47e-08;sequence=TATTAATAACA;
-phiX174	fimo	polypeptide_motif	4303	4313	78.2	+	.	Name=1;ID=1-59-phiX174;pvalue=1.52e-08;sequence=TTGATATTAAT;
-phiX174	fimo	polypeptide_motif	5033	5043	 78	+	.	Name=1;ID=1-60-phiX174;pvalue=1.58e-08;sequence=GTCAGATATGG;
-phiX174	fimo	polypeptide_motif	2579	2589	77.6	+	.	Name=1;ID=1-61-phiX174;pvalue=1.73e-08;sequence=TGGATACATCT;
-phiX174	fimo	polypeptide_motif	322	332	77.4	+	.	Name=1;ID=1-62-phiX174;pvalue=1.82e-08;sequence=GACATTTTAAA;
-phiX174	fimo	polypeptide_motif	5001	5011	76.8	+	.	Name=1;ID=1-63-phiX174;pvalue=2.09e-08;sequence=GGTTTCTATGT;
-phiX174	fimo	polypeptide_motif	4217	4227	76.7	+	.	Name=1;ID=1-64-phiX174;pvalue=2.15e-08;sequence=TGCTTCTGACG;
-phiX174	fimo	polypeptide_motif	4262	4272	76.6	+	.	Name=1;ID=1-65-phiX174;pvalue=2.18e-08;sequence=AATGGATGAAT;
-phiX174	fimo	polypeptide_motif	3569	3579	76.5	+	.	Name=1;ID=1-66-phiX174;pvalue=2.26e-08;sequence=TATGGAAAACA;
-phiX174	fimo	polypeptide_motif	194	204	76.4	+	.	Name=1;ID=1-67-phiX174;pvalue=2.29e-08;sequence=ATCAACTAACG;
-phiX174	fimo	polypeptide_motif	131	141	 76	+	.	Name=1;ID=1-68-phiX174;pvalue=2.49e-08;sequence=AAATGAGAAAA;
-phiX174	fimo	polypeptide_motif	1491	1501	75.9	+	.	Name=1;ID=1-69-phiX174;pvalue=2.55e-08;sequence=GCCATCTCAAA;
-phiX174	fimo	polypeptide_motif	434	444	75.7	+	.	Name=1;ID=1-70-phiX174;pvalue=2.67e-08;sequence=GGCCTCTATTA;
-phiX174	fimo	polypeptide_motif	4565	4575	75.6	+	.	Name=1;ID=1-71-phiX174;pvalue=2.73e-08;sequence=TTGGTTTATCG;
-phiX174	fimo	polypeptide_motif	102	112	75.6	+	.	Name=1;ID=1-72-phiX174;pvalue=2.75e-08;sequence=GAATTAAATCG;
-phiX174	fimo	polypeptide_motif	903	913	75.5	+	.	Name=1;ID=1-73-phiX174;pvalue=2.82e-08;sequence=GAGGTACTAAA;
-phiX174	fimo	polypeptide_motif	4748	4758	75.2	+	.	Name=1;ID=1-74-phiX174;pvalue=3.01e-08;sequence=TACAGCTAATG;
-phiX174	fimo	polypeptide_motif	2622	2632	 75	+	.	Name=1;ID=1-75-phiX174;pvalue=3.16e-08;sequence=TGCTGATATTG;
-phiX174	fimo	polypeptide_motif	467	477	74.7	+	.	Name=1;ID=1-76-phiX174;pvalue=3.35e-08;sequence=TTTGGATTTAA;
-phiX174	fimo	polypeptide_motif	4033	4043	74.6	+	.	Name=1;ID=1-77-phiX174;pvalue=3.44e-08;sequence=AGCGTATCGAG;
-phiX174	fimo	polypeptide_motif	1348	1358	74.6	+	.	Name=1;ID=1-78-phiX174;pvalue=3.46e-08;sequence=TACCAATAAAA;
-phiX174	fimo	polypeptide_motif	239	249	74.4	+	.	Name=1;ID=1-79-phiX174;pvalue=3.62e-08;sequence=AGTGGCTTAAT;
-phiX174	fimo	polypeptide_motif	500	510	74.1	+	.	Name=1;ID=1-80-phiX174;pvalue=3.84e-08;sequence=GACGAGTAACA;
-phiX174	fimo	polypeptide_motif	3001	3011	 74	+	.	Name=1;ID=1-81-phiX174;pvalue=3.93e-08;sequence=GCGGTCAAAAA;
-phiX174	fimo	polypeptide_motif	3776	3786	 74	+	.	Name=1;ID=1-82-phiX174;pvalue=3.98e-08;sequence=TATTTCTAATG;
-phiX174	fimo	polypeptide_motif	2026	2036	73.9	+	.	Name=1;ID=1-83-phiX174;pvalue=4.06e-08;sequence=GAAGTTTAAGA;
-phiX174	fimo	polypeptide_motif	4237	4247	73.8	+	.	Name=1;ID=1-84-phiX174;pvalue=4.12e-08;sequence=AGTTTGTATCT;
-phiX174	fimo	polypeptide_motif	803	813	73.7	+	.	Name=1;ID=1-85-phiX174;pvalue=4.24e-08;sequence=AGAAGAAAACG;
-phiX174	fimo	polypeptide_motif	3770	3780	73.6	+	.	Name=1;ID=1-86-phiX174;pvalue=4.35e-08;sequence=AAAGGATATTT;
-phiX174	fimo	polypeptide_motif	3429	3439	73.5	+	.	Name=1;ID=1-87-phiX174;pvalue=4.45e-08;sequence=GAGATGCAAAA;
-phiX174	fimo	polypeptide_motif	99	109	73.5	+	.	Name=1;ID=1-88-phiX174;pvalue=4.48e-08;sequence=TACGAATTAAA;
-phiX174	fimo	polypeptide_motif	67	77	73.2	+	.	Name=1;ID=1-89-phiX174;pvalue=4.78e-08;sequence=TCTTGATAAAG;
-phiX174	fimo	polypeptide_motif	5332	5342	72.9	+	.	Name=1;ID=1-90-phiX174;pvalue=5.13e-08;sequence=ATCTGCTCAAA;
-phiX174	fimo	polypeptide_motif	277	287	72.9	+	.	Name=1;ID=1-91-phiX174;pvalue=5.14e-08;sequence=TTTAGATATGA;
-phiX174	fimo	polypeptide_motif	4338	4348	72.8	+	.	Name=1;ID=1-92-phiX174;pvalue=5.18e-08;sequence=GGGGACGAAAA;
-phiX174	fimo	polypeptide_motif	3812	3822	72.8	+	.	Name=1;ID=1-93-phiX174;pvalue=5.28e-08;sequence=GGTTGATATTT;
-phiX174	fimo	polypeptide_motif	1909	1919	72.6	+	.	Name=1;ID=1-94-phiX174;pvalue=5.51e-08;sequence=TAACGCTAAAG;
-phiX174	fimo	polypeptide_motif	3000	3010	72.6	+	.	Name=1;ID=1-95-phiX174;pvalue=5.54e-08;sequence=GGCGGTCAAAA;
-phiX174	fimo	polypeptide_motif	3891	3901	72.4	+	.	Name=1;ID=1-96-phiX174;pvalue=5.75e-08;sequence=ATTGGCTCTAA;
-phiX174	fimo	polypeptide_motif	3079	3089	72.4	+	.	Name=1;ID=1-97-phiX174;pvalue=5.76e-08;sequence=CTGGTATTAAA;
-phiX174	fimo	polypeptide_motif	37	47	72.4	+	.	Name=1;ID=1-98-phiX174;pvalue=5.79e-08;sequence=TTCGGATATTT;
-phiX174	fimo	polypeptide_motif	380	390	72.2	+	.	Name=1;ID=1-99-phiX174;pvalue=6.01e-08;sequence=GTAAGAAATCA;
diff -r 34c794383f81 -r 62d1fae3b7d3 test-data/fimo_output_html_1.html
--- a/test-data/fimo_output_html_1.html	Fri Mar 18 08:23:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-<!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 34c794383f81 -r 62d1fae3b7d3 test-data/fimo_output_html_2.html
--- a/test-data/fimo_output_html_2.html	Fri Mar 18 08:23:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-<!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 34c794383f81 -r 62d1fae3b7d3 test-data/fimo_output_interval_1.txt
--- a/test-data/fimo_output_interval_1.txt	Fri Mar 18 08:23:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-#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 34c794383f81 -r 62d1fae3b7d3 test-data/fimo_output_interval_2.txt
--- a/test-data/fimo_output_interval_2.txt	Fri Mar 18 08:23:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-#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 34c794383f81 -r 62d1fae3b7d3 test-data/fimo_output_txt_1.txt
--- a/test-data/fimo_output_txt_1.txt	Fri Mar 18 08:23:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-#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 34c794383f81 -r 62d1fae3b7d3 test-data/fimo_output_txt_2.txt
--- a/test-data/fimo_output_txt_2.txt	Fri Mar 18 08:23:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,100 +0,0 @@
-#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 34c794383f81 -r 62d1fae3b7d3 test-data/fimo_output_xml_1.xml
--- a/test-data/fimo_output_xml_1.xml	Fri Mar 18 08:23:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!-- Begin document body -->
-<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 34c794383f81 -r 62d1fae3b7d3 test-data/fimo_output_xml_2.xml
--- a/test-data/fimo_output_xml_2.xml	Fri Mar 18 08:23:54 2016 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,74 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?>
-<!-- Begin document body -->
-<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 34c794383f81 -r 62d1fae3b7d3 test-data/meme_output_html_1.html
--- a/test-data/meme_output_html_1.html	Fri Mar 18 08:23:54 2016 -0400
+++ b/test-data/meme_output_html_1.html	Fri Jun 17 13:16:52 2016 -0400
@@ -12,9 +12,6 @@
         "stop_reason": "Stopped because requested number of motifs (1) found.",
         "cmd": [
           "meme",
-          "/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat",
-          "-o",
-          "/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1912/dataset_2530_files",
           "-nostatus"
         ],
         "options": {
diff -r 34c794383f81 -r 62d1fae3b7d3 test-data/meme_output_html_2.html
--- a/test-data/meme_output_html_2.html	Fri Mar 18 08:23:54 2016 -0400
+++ b/test-data/meme_output_html_2.html	Fri Jun 17 13:16:52 2016 -0400
@@ -12,15 +12,6 @@
         "stop_reason": "Stopped because requested number of motifs (1) found.",
         "cmd": [
           "meme",
-          "/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat",
-          "-o",
-          "/Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1929/dataset_2578_files",
-          "-nostatus", "-sf", "Galaxy_FASTA_Input", "-dna", "-mod", "zoops",
-          "-nmotifs", "1", "-wnsites", "0.8", "-minw", "8", "-maxw", "50",
-          "-wg", "11", "-ws", "1", "-maxiter", "50", "-distance", "0.001",
-          "-prior", "dirichlet", "-b", "0.01", "-plib",
-          "/Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2577.dat",
-          "-spmap", "uni", "-spfuzz", "0.5"
         ],
         "options": {
           "mod": "zoops",
diff -r 34c794383f81 -r 62d1fae3b7d3 test-data/meme_output_txt_1.txt
--- a/test-data/meme_output_txt_1.txt	Fri Mar 18 08:23:54 2016 -0400
+++ b/test-data/meme_output_txt_1.txt	Fri Jun 17 13:16:52 2016 -0400
@@ -28,7 +28,7 @@
 ********************************************************************************
 TRAINING SET
 ********************************************************************************
-DATAFILE= /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat
+DATAFILE=
 ALPHABET= ACDEFGHIKLMNPQRSTVWY
 Sequence name            Weight Length  Sequence name            Weight Length  
 -------------            ------ ------  -------------            ------ ------  
@@ -55,7 +55,7 @@
 This information can also be useful in the event you wish to report a
 problem with the MEME software.
 
-command: meme /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat -o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1912/dataset_2530_files -nostatus 
+command: meme 
 
 model:  mod=         zoops    nmotifs=         1    evt=           inf
 object function=  E-value of product of p-values
@@ -267,7 +267,7 @@
 
 
 
-Time  0.53 secs.
+Time
 
 ********************************************************************************
 
@@ -320,6 +320,6 @@
 Stopped because requested number of motifs (1) found.
 ********************************************************************************
 
-CPU: MacBook-Pro-2.local
+CPU:
 
 ********************************************************************************
diff -r 34c794383f81 -r 62d1fae3b7d3 test-data/meme_output_txt_2.txt
--- a/test-data/meme_output_txt_2.txt	Fri Mar 18 08:23:54 2016 -0400
+++ b/test-data/meme_output_txt_2.txt	Fri Jun 17 13:16:52 2016 -0400
@@ -55,7 +55,7 @@
 This information can also be useful in the event you wish to report a
 problem with the MEME software.
 
-command: meme /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2490.dat -o /Users/gvk/work/git_workspace/galaxy/database/job_working_directory/001/1929/dataset_2578_files -nostatus -sf Galaxy_FASTA_Input -dna -mod zoops -nmotifs 1 -wnsites 0.8 -minw 8 -maxw 50 -wg 11 -ws 1 -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -plib /Users/gvk/work/git_workspace/galaxy/database/files/002/dataset_2577.dat -spmap uni -spfuzz 0.5 
+command: meme 
 
 model:  mod=         zoops    nmotifs=         1    evt=           inf
 object function=  E-value of product of p-values
@@ -69,7 +69,7 @@
 data:   n=            1500    N=              30    shuffle=        -1
 strands: +
 sample: seed=            0    ctfrac=         -1    maxwords=       -1
-Dirichlet mixture priors file: dataset_2577.dat
+Dirichlet mixture priors file:
 Letter frequencies in dataset:
 A 0.294 C 0.231 G 0.257 T 0.217 
 Background letter frequencies (from dataset with add-one prior applied):
@@ -261,7 +261,7 @@
 
 
 
-Time  0.17 secs.
+Time  
 
 ********************************************************************************
 
@@ -314,6 +314,6 @@
 Stopped because requested number of motifs (1) found.
 ********************************************************************************
 
-CPU: dot1x-cb-51.aset.psu.edu
+CPU:
 
 ********************************************************************************
diff -r 34c794383f81 -r 62d1fae3b7d3 test-data/motif1.gff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/motif1.gff	Fri Jun 17 13:16:52 2016 -0400
@@ -0,0 +1,100 @@
+##gff-version 3
+phiX174	fimo	polypeptide_motif	1	11	78.3	+	.	Name=1;ID=1-57-phiX174;pvalue=1.46e-08;sequence=GAGTTTTATCG;
+phiX174	fimo	polypeptide_motif	3	13	57.5	+	.	Name=1;ID=1-471-phiX174;pvalue=1.79e-06;sequence=GTTTTATCGCT;
+phiX174	fimo	polypeptide_motif	7	17	 45	+	.	Name=1;ID=1-1378-phiX174;pvalue=3.18e-05;sequence=TATCGCTTCCA;
+phiX174	fimo	polypeptide_motif	10	20	53.9	+	.	Name=1;ID=1-605-phiX174;pvalue=4.1e-06;sequence=CGCTTCCATGA;
+phiX174	fimo	polypeptide_motif	17	27	40.2	+	.	Name=1;ID=1-1887-phiX174;pvalue=9.55e-05;sequence=ATGACGCAGAA;
+phiX174	fimo	polypeptide_motif	18	28	45.3	+	.	Name=1;ID=1-1349-phiX174;pvalue=2.98e-05;sequence=TGACGCAGAAG;
+phiX174	fimo	polypeptide_motif	19	29	55.8	+	.	Name=1;ID=1-527-phiX174;pvalue=2.6e-06;sequence=GACGCAGAAGT;
+phiX174	fimo	polypeptide_motif	21	31	41.5	+	.	Name=1;ID=1-1705-phiX174;pvalue=7.07e-05;sequence=CGCAGAAGTTA;
+phiX174	fimo	polypeptide_motif	22	32	44.6	+	.	Name=1;ID=1-1404-phiX174;pvalue=3.44e-05;sequence=GCAGAAGTTAA;
+phiX174	fimo	polypeptide_motif	24	34	79.1	+	.	Name=1;ID=1-53-phiX174;pvalue=1.23e-08;sequence=AGAAGTTAACA;
+phiX174	fimo	polypeptide_motif	25	35	45.3	+	.	Name=1;ID=1-1347-phiX174;pvalue=2.97e-05;sequence=GAAGTTAACAC;
+phiX174	fimo	polypeptide_motif	26	36	59.2	+	.	Name=1;ID=1-417-phiX174;pvalue=1.19e-06;sequence=AAGTTAACACT;
+phiX174	fimo	polypeptide_motif	30	40	44.7	+	.	Name=1;ID=1-1399-phiX174;pvalue=3.4e-05;sequence=TAACACTTTCG;
+phiX174	fimo	polypeptide_motif	37	47	72.4	+	.	Name=1;ID=1-98-phiX174;pvalue=5.79e-08;sequence=TTCGGATATTT;
+phiX174	fimo	polypeptide_motif	39	49	65.3	+	.	Name=1;ID=1-213-phiX174;pvalue=2.92e-07;sequence=CGGATATTTCT;
+phiX174	fimo	polypeptide_motif	41	51	55.3	+	.	Name=1;ID=1-548-phiX174;pvalue=2.97e-06;sequence=GATATTTCTGA;
+phiX174	fimo	polypeptide_motif	43	53	58.4	+	.	Name=1;ID=1-442-phiX174;pvalue=1.43e-06;sequence=TATTTCTGATG;
+phiX174	fimo	polypeptide_motif	46	56	53.7	+	.	Name=1;ID=1-617-phiX174;pvalue=4.23e-06;sequence=TTCTGATGAGT;
+phiX174	fimo	polypeptide_motif	50	60	45.4	+	.	Name=1;ID=1-1333-phiX174;pvalue=2.86e-05;sequence=GATGAGTCGAA;
+phiX174	fimo	polypeptide_motif	51	61	48.4	+	.	Name=1;ID=1-1094-phiX174;pvalue=1.44e-05;sequence=ATGAGTCGAAA;
+phiX174	fimo	polypeptide_motif	52	62	83.9	+	.	Name=1;ID=1-22-phiX174;pvalue=4.06e-09;sequence=TGAGTCGAAAA;
+phiX174	fimo	polypeptide_motif	53	63	53.9	+	.	Name=1;ID=1-601-phiX174;pvalue=4.03e-06;sequence=GAGTCGAAAAA;
+phiX174	fimo	polypeptide_motif	54	64	62.9	+	.	Name=1;ID=1-297-phiX174;pvalue=5.16e-07;sequence=AGTCGAAAAAT;
+phiX174	fimo	polypeptide_motif	55	65	52.8	+	.	Name=1;ID=1-675-phiX174;pvalue=5.26e-06;sequence=GTCGAAAAATT;
+phiX174	fimo	polypeptide_motif	56	66	41.4	+	.	Name=1;ID=1-1713-phiX174;pvalue=7.2e-05;sequence=TCGAAAAATTA;
+phiX174	fimo	polypeptide_motif	58	68	43.4	+	.	Name=1;ID=1-1500-phiX174;pvalue=4.56e-05;sequence=GAAAAATTATC;
+phiX174	fimo	polypeptide_motif	59	69	59.6	+	.	Name=1;ID=1-409-phiX174;pvalue=1.1e-06;sequence=AAAAATTATCT;
+phiX174	fimo	polypeptide_motif	61	71	61.8	+	.	Name=1;ID=1-329-phiX174;pvalue=6.52e-07;sequence=AAATTATCTTG;
+phiX174	fimo	polypeptide_motif	63	73	59.2	+	.	Name=1;ID=1-419-phiX174;pvalue=1.2e-06;sequence=ATTATCTTGAT;
+phiX174	fimo	polypeptide_motif	65	75	53.3	+	.	Name=1;ID=1-643-phiX174;pvalue=4.66e-06;sequence=TATCTTGATAA;
+phiX174	fimo	polypeptide_motif	66	76	51.8	+	.	Name=1;ID=1-737-phiX174;pvalue=6.54e-06;sequence=ATCTTGATAAA;
+phiX174	fimo	polypeptide_motif	67	77	73.2	+	.	Name=1;ID=1-89-phiX174;pvalue=4.78e-08;sequence=TCTTGATAAAG;
+phiX174	fimo	polypeptide_motif	69	79	63.8	+	.	Name=1;ID=1-268-phiX174;pvalue=4.15e-07;sequence=TTGATAAAGCA;
+phiX174	fimo	polypeptide_motif	71	81	40.2	+	.	Name=1;ID=1-1882-phiX174;pvalue=9.49e-05;sequence=GATAAAGCAGG;
+phiX174	fimo	polypeptide_motif	73	83	45.4	+	.	Name=1;ID=1-1334-phiX174;pvalue=2.87e-05;sequence=TAAAGCAGGAA;
+phiX174	fimo	polypeptide_motif	74	84	50.9	+	.	Name=1;ID=1-832-phiX174;pvalue=8.05e-06;sequence=AAAGCAGGAAT;
+phiX174	fimo	polypeptide_motif	76	86	52.2	+	.	Name=1;ID=1-710-phiX174;pvalue=5.96e-06;sequence=AGCAGGAATTA;
+phiX174	fimo	polypeptide_motif	78	88	51.8	+	.	Name=1;ID=1-741-phiX174;pvalue=6.65e-06;sequence=CAGGAATTACT;
+phiX174	fimo	polypeptide_motif	79	89	 45	+	.	Name=1;ID=1-1369-phiX174;pvalue=3.16e-05;sequence=AGGAATTACTA;
+phiX174	fimo	polypeptide_motif	80	90	43.3	+	.	Name=1;ID=1-1511-phiX174;pvalue=4.63e-05;sequence=GGAATTACTAC;
+phiX174	fimo	polypeptide_motif	81	91	59.8	+	.	Name=1;ID=1-402-phiX174;pvalue=1.05e-06;sequence=GAATTACTACT;
+phiX174	fimo	polypeptide_motif	82	92	46.9	+	.	Name=1;ID=1-1205-phiX174;pvalue=2.03e-05;sequence=AATTACTACTG;
+phiX174	fimo	polypeptide_motif	88	98	41.2	+	.	Name=1;ID=1-1744-phiX174;pvalue=7.51e-05;sequence=TACTGCTTGTT;
+phiX174	fimo	polypeptide_motif	91	101	53.6	+	.	Name=1;ID=1-621-phiX174;pvalue=4.33e-06;sequence=TGCTTGTTTAC;
+phiX174	fimo	polypeptide_motif	92	102	44.8	+	.	Name=1;ID=1-1388-phiX174;pvalue=3.31e-05;sequence=GCTTGTTTACG;
+phiX174	fimo	polypeptide_motif	93	103	43.2	+	.	Name=1;ID=1-1525-phiX174;pvalue=4.82e-05;sequence=CTTGTTTACGA;
+phiX174	fimo	polypeptide_motif	95	105	61.9	+	.	Name=1;ID=1-327-phiX174;pvalue=6.5e-07;sequence=TGTTTACGAAT;
+phiX174	fimo	polypeptide_motif	96	106	42.9	+	.	Name=1;ID=1-1553-phiX174;pvalue=5.08e-05;sequence=GTTTACGAATT;
+phiX174	fimo	polypeptide_motif	98	108	45.4	+	.	Name=1;ID=1-1340-phiX174;pvalue=2.9e-05;sequence=TTACGAATTAA;
+phiX174	fimo	polypeptide_motif	99	109	73.5	+	.	Name=1;ID=1-88-phiX174;pvalue=4.48e-08;sequence=TACGAATTAAA;
+phiX174	fimo	polypeptide_motif	100	110	 53	+	.	Name=1;ID=1-661-phiX174;pvalue=4.99e-06;sequence=ACGAATTAAAT;
+phiX174	fimo	polypeptide_motif	102	112	75.6	+	.	Name=1;ID=1-72-phiX174;pvalue=2.75e-08;sequence=GAATTAAATCG;
+phiX174	fimo	polypeptide_motif	104	114	52.2	+	.	Name=1;ID=1-713-phiX174;pvalue=6.05e-06;sequence=ATTAAATCGAA;
+phiX174	fimo	polypeptide_motif	106	116	59.6	+	.	Name=1;ID=1-407-phiX174;pvalue=1.09e-06;sequence=TAAATCGAAGT;
+phiX174	fimo	polypeptide_motif	112	122	41.6	+	.	Name=1;ID=1-1683-phiX174;pvalue=6.85e-05;sequence=GAAGTGGACTG;
+phiX174	fimo	polypeptide_motif	114	124	45.3	+	.	Name=1;ID=1-1342-phiX174;pvalue=2.92e-05;sequence=AGTGGACTGCT;
+phiX174	fimo	polypeptide_motif	118	128	56.2	+	.	Name=1;ID=1-512-phiX174;pvalue=2.38e-06;sequence=GACTGCTGGCG;
+phiX174	fimo	polypeptide_motif	122	132	51.4	+	.	Name=1;ID=1-774-phiX174;pvalue=7.15e-06;sequence=GCTGGCGGAAA;
+phiX174	fimo	polypeptide_motif	123	133	43.1	+	.	Name=1;ID=1-1533-phiX174;pvalue=4.93e-05;sequence=CTGGCGGAAAA;
+phiX174	fimo	polypeptide_motif	124	134	48.6	+	.	Name=1;ID=1-1085-phiX174;pvalue=1.38e-05;sequence=TGGCGGAAAAT;
+phiX174	fimo	polypeptide_motif	125	135	68.3	+	.	Name=1;ID=1-146-phiX174;pvalue=1.49e-07;sequence=GGCGGAAAATG;
+phiX174	fimo	polypeptide_motif	126	136	46.4	+	.	Name=1;ID=1-1243-phiX174;pvalue=2.27e-05;sequence=GCGGAAAATGA;
+phiX174	fimo	polypeptide_motif	128	138	58.3	+	.	Name=1;ID=1-446-phiX174;pvalue=1.48e-06;sequence=GGAAAATGAGA;
+phiX174	fimo	polypeptide_motif	129	139	43.2	+	.	Name=1;ID=1-1522-phiX174;pvalue=4.78e-05;sequence=GAAAATGAGAA;
+phiX174	fimo	polypeptide_motif	130	140	54.1	+	.	Name=1;ID=1-595-phiX174;pvalue=3.92e-06;sequence=AAAATGAGAAA;
+phiX174	fimo	polypeptide_motif	131	141	 76	+	.	Name=1;ID=1-68-phiX174;pvalue=2.49e-08;sequence=AAATGAGAAAA;
+phiX174	fimo	polypeptide_motif	132	142	51.2	+	.	Name=1;ID=1-800-phiX174;pvalue=7.57e-06;sequence=AATGAGAAAAT;
+phiX174	fimo	polypeptide_motif	133	143	56.2	+	.	Name=1;ID=1-513-phiX174;pvalue=2.41e-06;sequence=ATGAGAAAATT;
+phiX174	fimo	polypeptide_motif	134	144	41.1	+	.	Name=1;ID=1-1761-phiX174;pvalue=7.83e-05;sequence=TGAGAAAATTC;
+phiX174	fimo	polypeptide_motif	135	145	50.3	+	.	Name=1;ID=1-910-phiX174;pvalue=9.39e-06;sequence=GAGAAAATTCG;
+phiX174	fimo	polypeptide_motif	136	146	43.3	+	.	Name=1;ID=1-1517-phiX174;pvalue=4.66e-05;sequence=AGAAAATTCGA;
+phiX174	fimo	polypeptide_motif	139	149	54.2	+	.	Name=1;ID=1-588-phiX174;pvalue=3.75e-06;sequence=AAATTCGACCT;
+phiX174	fimo	polypeptide_motif	141	151	42.2	+	.	Name=1;ID=1-1625-phiX174;pvalue=6.01e-05;sequence=ATTCGACCTAT;
+phiX174	fimo	polypeptide_motif	143	153	 50	+	.	Name=1;ID=1-938-phiX174;pvalue=9.94e-06;sequence=TCGACCTATCC;
+phiX174	fimo	polypeptide_motif	145	155	44.6	+	.	Name=1;ID=1-1403-phiX174;pvalue=3.42e-05;sequence=GACCTATCCTT;
+phiX174	fimo	polypeptide_motif	155	165	51.3	+	.	Name=1;ID=1-787-phiX174;pvalue=7.35e-06;sequence=TGCGCAGCTCG;
+phiX174	fimo	polypeptide_motif	157	167	51.1	+	.	Name=1;ID=1-807-phiX174;pvalue=7.68e-06;sequence=CGCAGCTCGAG;
+phiX174	fimo	polypeptide_motif	159	169	44.5	+	.	Name=1;ID=1-1420-phiX174;pvalue=3.56e-05;sequence=CAGCTCGAGAA;
+phiX174	fimo	polypeptide_motif	160	170	 40	+	.	Name=1;ID=1-1921-phiX174;pvalue=9.89e-05;sequence=AGCTCGAGAAG;
+phiX174	fimo	polypeptide_motif	166	176	60.9	+	.	Name=1;ID=1-365-phiX174;pvalue=8.02e-07;sequence=AGAAGCTCTTA;
+phiX174	fimo	polypeptide_motif	168	178	62.3	+	.	Name=1;ID=1-311-phiX174;pvalue=5.87e-07;sequence=AAGCTCTTACT;
+phiX174	fimo	polypeptide_motif	181	191	49.9	+	.	Name=1;ID=1-946-phiX174;pvalue=1.01e-05;sequence=GCGACCTTTCG;
+phiX174	fimo	polypeptide_motif	187	197	52.5	+	.	Name=1;ID=1-694-phiX174;pvalue=5.64e-06;sequence=TTTCGCCATCA;
+phiX174	fimo	polypeptide_motif	191	201	46.6	+	.	Name=1;ID=1-1232-phiX174;pvalue=2.2e-05;sequence=GCCATCAACTA;
+phiX174	fimo	polypeptide_motif	194	204	76.4	+	.	Name=1;ID=1-67-phiX174;pvalue=2.29e-08;sequence=ATCAACTAACG;
+phiX174	fimo	polypeptide_motif	201	211	40.1	+	.	Name=1;ID=1-1908-phiX174;pvalue=9.77e-05;sequence=AACGATTCTGT;
+phiX174	fimo	polypeptide_motif	203	213	 63	+	.	Name=1;ID=1-291-phiX174;pvalue=5e-07;sequence=CGATTCTGTCA;
+phiX174	fimo	polypeptide_motif	205	215	53.8	+	.	Name=1;ID=1-610-phiX174;pvalue=4.16e-06;sequence=ATTCTGTCAAA;
+phiX174	fimo	polypeptide_motif	206	216	59.1	+	.	Name=1;ID=1-421-phiX174;pvalue=1.23e-06;sequence=TTCTGTCAAAA;
+phiX174	fimo	polypeptide_motif	207	217	 68	+	.	Name=1;ID=1-153-phiX174;pvalue=1.58e-07;sequence=TCTGTCAAAAA;
+phiX174	fimo	polypeptide_motif	209	219	49.6	+	.	Name=1;ID=1-988-phiX174;pvalue=1.09e-05;sequence=TGTCAAAAACT;
+phiX174	fimo	polypeptide_motif	210	220	40.8	+	.	Name=1;ID=1-1810-phiX174;pvalue=8.33e-05;sequence=GTCAAAAACTG;
+phiX174	fimo	polypeptide_motif	213	223	59.7	+	.	Name=1;ID=1-404-phiX174;pvalue=1.06e-06;sequence=AAAAACTGACG;
+phiX174	fimo	polypeptide_motif	223	233	 42	+	.	Name=1;ID=1-1654-phiX174;pvalue=6.36e-05;sequence=GCGTTGGATGA;
+phiX174	fimo	polypeptide_motif	225	235	61.4	+	.	Name=1;ID=1-349-phiX174;pvalue=7.16e-07;sequence=GTTGGATGAGG;
+phiX174	fimo	polypeptide_motif	227	237	40.3	+	.	Name=1;ID=1-1874-phiX174;pvalue=9.32e-05;sequence=TGGATGAGGAG;
+phiX174	fimo	polypeptide_motif	228	238	49.9	+	.	Name=1;ID=1-947-phiX174;pvalue=1.01e-05;sequence=GGATGAGGAGA;
+phiX174	fimo	polypeptide_motif	229	239	 45	+	.	Name=1;ID=1-1370-phiX174;pvalue=3.16e-05;sequence=GATGAGGAGAA;
+phiX174	fimo	polypeptide_motif	230	240	44.8	+	.	Name=1;ID=1-1395-phiX174;pvalue=3.33e-05;sequence=ATGAGGAGAAG;
diff -r 34c794383f81 -r 62d1fae3b7d3 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Mar 18 08:23:54 2016 -0400
+++ b/tool_dependencies.xml	Fri Jun 17 13:16:52 2016 -0400
@@ -4,6 +4,6 @@
         <repository changeset_revision="942ae5bafee3" name="package_imagemagick_6_9_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="meme" version="4.11.0">
-        <repository changeset_revision="738dc831aeac" name="package_meme_4_11_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="5774a0e96d6f" name="package_meme_4_11_0" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
 </tool_dependency>