# HG changeset patch
# User iuc
# Date 1450821731 18000
# Node ID d20e391eb22ff2973d1bbbdb2e8f94d2d1cde616
# Parent  e416c7c26977edd320f09eb03b9895788201c3ea
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meme commit e96df94dba60050fa28aaf55b5bb095717a5f260

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
@@ -0,0 +1,100 @@
+##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 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
@@ -0,0 +1,100 @@
+##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 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
@@ -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_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"?>
+<!-- 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 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"?>
+<!-- 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 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>
+    <!-- Locations of all fasta files under genome directory -->
+    <table name="all_fasta" comment_char="#">
+        <columns>value, dbkey, name, path</columns>
+        <file path="tool-data/all_fasta.loc" />
+    </table>
+</tables>