# HG changeset patch
# User jjohnson
# Date 1411668316 14400
# Node ID 87f7630ab82ffec7b0c7b233ed38807d27390470
Imported from capsule None
diff -r 000000000000 -r 87f7630ab82f misp.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/misp.xml Thu Sep 25 14:05:16 2014 -0400
@@ -0,0 +1,136 @@
+
+ Input one or more motifs, find all hits in peak regions
+
+ misp
+ bedtools
+
+
+#if $motifopt.motifopt_select == "upload"
+ #set $motif_db = str($motifopt.motif_file)
+#else
+ #set $motif_db = "\${MISP_DATABASE_PATH}/motif/cistrome.db"
+#end if
+#set $motif_id = str($motifopt.motif_id)
+#if $refGenomeSource.genomeSource == "history":
+ #set $genome_file = $refGenomeSource.ownFile
+#else:
+ #set $genome_file = $refGenomeSource.index.fields.path
+#end if
+bedtools getfasta -fi $genome_file -bed $bedfile -fo out.fasta > /dev/null &&
+misp out.fasta $motif_db $pvalue $motif_id output &> $log &&
+cat output* > $outputtxt
+
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+Given a motif, this tool will find all hits of the motif in specified region.
+
+-----
+
+**Formula**
+
+.. image:: ./static/cistrome_icons/misp_formula.png
+
+-----
+
+**TIP:** The source code of misp is available at bitbucket_
+
+.. _bitbucket: https://bitbucket.org/hanfeisun/misp/overview
+
+
+**TIP:** To check the motif id in our database, click here_
+
+.. _here: http://cistrome.org/motif/
+
+-----
+
+Left to right shoule be:
+
+T
+
+C
+
+G
+
+A
+
+**Example of the format of uploaded motif database.**
+
+M00139
+
+0.667 0.111 0.667 0.01 0.01 0.01 0.01 0.01 0.333 0.01 0.01 0.333 0.444 0.222 0.01 0.01 0.01 0.01
+
+0.01 0.546 0.111 0.97 0.01 0.97 0.01 0.97 0.111 0.01 0.444 0.444 0.536 0.333 0.222 0.111 0.01 0.222
+
+0.01 0.333 0.111 0.01 0.01 0.01 0.97 0.01 0.222 0.01 0.536 0.111 0.01 0.333 0.758 0.556 0.667 0.667
+
+0.313 0.01 0.111 0.01 0.97 0.01 0.01 0.01 0.334 0.97 0.01 0.112 0.01 0.112 0.01 0.323 0.313 0.101
+
+hPDI060
+
+0.01 0.01 0.01 0.625 0.01 0.01
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+0.97 0.97 0.97 0.01 0.5 0.97
+
+0.01 0.01 0.01 0.01 0.48 0.01
+
+0.01 0.01 0.01 0.355 0.01 0.01
+
+
+
diff -r 000000000000 -r 87f7630ab82f test-data/misp.hits
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/misp.hits Thu Sep 25 14:05:16 2014 -0400
@@ -0,0 +1,13 @@
+# Parameter List:
+# Input sequence: out.fasta
+# Output path: output
+# P value: 0.001
+# CG percent: 0.54
+# tolerance: 8.87
+# factor ID: M00139
+sequence_name sequence_length hits_score hits_position sequence
+chr19:108-504 396 0.18 81 TCCCACACTCGTTGGCAG
+chr19:3876-4233 357 * 0 *
+chr19:3345-5762 2417 1.31 1850 TCTCTCGGGAGTTTGGGG
+chr19:6337-6943 606 0.06 55(-) ctaccaccatccgtgagt
+chr19:13013-13650 637 * 0 *
diff -r 000000000000 -r 87f7630ab82f test-data/misp.log
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/misp.log Thu Sep 25 14:05:16 2014 -0400
@@ -0,0 +1,4 @@
+Calculating Background..
+A or T: 2048
+C or G: 2365
+Others: 0
diff -r 000000000000 -r 87f7630ab82f test-data/misp_motif
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/misp_motif Thu Sep 25 14:05:16 2014 -0400
@@ -0,0 +1,5 @@
+M00139
+0.667 0.111 0.667 0.01 0.01 0.01 0.01 0.01 0.333 0.01 0.01 0.333 0.444 0.222 0.01 0.01 0.01 0.01
+0.01 0.546 0.111 0.97 0.01 0.97 0.01 0.97 0.111 0.01 0.444 0.444 0.536 0.333 0.222 0.111 0.01 0.222
+0.01 0.333 0.111 0.01 0.01 0.01 0.97 0.01 0.222 0.01 0.536 0.111 0.01 0.333 0.758 0.556 0.667 0.667
+0.313 0.01 0.111 0.01 0.97 0.01 0.01 0.01 0.334 0.97 0.01 0.112 0.01 0.112 0.01 0.323 0.313 0.101
diff -r 000000000000 -r 87f7630ab82f test-data/mm9_chr19_part.fasta
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/mm9_chr19_part.fasta Thu Sep 25 14:05:16 2014 -0400
@@ -0,0 +1,281 @@
+>chr19 mm9_chr19_3320000_3334000_+ chr19
+ATTGTTTCTTCTCTGGGATAGTAAACACTGCCAACTTTCCTTTCACTGGG
+TGCTCGGGAAGGCAAGGCAGAAGAAAACAGTGGAGTGGCCCCCAAAGTGG
+GACAGGCAGGGTACATTTCACAGGACATTTTCACTCTCTGGTGGGAACAG
+CGGGACACAGAAGAAGCCTCATGGACTCCAAGTTTCTTTTCCCACACTCG
+TTGGCAGCCTTGGGTTTGTTATCCTTGCGACAATGCCACTGTCCTCATGA
+AACCTGGTGACGTTGGCTGAGCAAATACTACCTCCGATATTGACTCAAAA
+CGTGTACAGGGGCTCAAAGTTCAAGTTCAGTGGGGCCTGAGGCTTGGAGG
+AGGAGGGGAAAACACTGCCTCCTGTGATTACAACATTCTTTAGTATGAAG
+TAGAGTTCCCTCAAAACTAGGTCTCATAGCCAAGTCCCCAAACGTCTTAA
+GCACTTTGGATAGATATCTATTGAGTCCTGCCAACCGGAAAGGAGGCTAG
+AGAGAATGACCATGGAGCAGCCATCCTCTTGGCAAAACAGTGGGGGCTGT
+GAAAATTCCCTGTCACATATATTAGGTGGGATAGTTAGGGTTGGGATGTT
+GTTTGGCCTTCTACACATAAGACCTTGGCTTCCAGCTCTAGTACTGAAAA
+AAAAACCAAACCAAAACAAAACAaaacaaacaaacaaacaaacaaaaaaa
+cGAgggctgtggtagctccgtggcagagcacctgactagcatgcatgcaa
+ccctacgattaatcAGCTTATCTTATTCTTTCCATtgtcctcaaacttga
+tatgtggccaaggacaatttgaacttcttgctgggatcacaagtgtgcat
+cattataccctctttatgtggtgtgggggatgggatctaggacttcatgc
+ctgctagacaagcgctgtaatactgagccacatccccagTTGTGGTTTGT
+TTTTTAGATTAAAAAtaatgtgtatgggaatgtatgaacatataaatgca
+ggtgcccatgatggccagaagggggagcaagatccccaggagctggagtt
+ataggtgtttgtgaacattgagacttggatgccgggaaccaaactgtggt
+cttgggcaagagtagtattcgtacttagttactgagcaatttcctccaac
+tcTGTTtttgttttgttttgttttgttttgttttggtttggtttggtttg
+gtttggtttggtttggtttggtttggtttggtttttgagacaggctcacg
+ctgtaacccaggctggtctccaactcatatatgatcctcctgcctcagtc
+tcccaagtaatgaaattacagatgtgagccaccacacAGGGCAAACGTAT
+CCATCGTGAGCAGCTGGCACAGTCTATGGGATTGAAACTGAGAAAGAATG
+TGAAAAATAAACAGGCGAGCTTGAGAAAGGTTATTCTAGCCTTGGTGCCA
+GTTCCTGGTATATTTTCAGCGCTCAGGGAGTTTAGGTTAATGCCCCAAGC
+TTCCCCATCCCCACCCCGAGGGGCGAGGGGGAGGTTAAGCTCTTTATTAA
+TAGCCACTCCGGGAGCTACAGTCCTTGGGAAAAGGGCTATGGTGAGGGTA
+GAGGAAGGAAAATGAGGTCCCCACAGGATAAAACCAGGTGCAGGCGGCTC
+TGGCTCATTATGGTGCCTCCCCAAGGCACGAGGTGTCTGAGAGTTCCTTC
+TGATGTTGTCTCCGCCCCTGCTCCTGTCCCTCCTGGCCGGCAGGGAGGGC
+CTGCTGTCAAGGCCGCTGAGCCTCCTGGACAGACAGGGCACAGGGCCAAT
+CCAGAGGGACGCAAAGCAGGACGCCAAGAAAAGAGGAAGTGTCCTTGGGG
+AGGGGACCGGTTAGGACTGGGGTTCTAGGGAGAGAAGGAAGGGCATTTAA
+GGTGAGTCCAACAGTCCAGGACTTAAAAGGAGCCTTAAGTAGGGGGCAGC
+AAGAGGTGACACTAGAGCCATCGAGGCCGATGAGGCCCGGGGGACAGCAG
+AAAGTGTTTCCAGATAGCACCTCTGCAGTGCCAGCCACATGTCACACTGG
+TCTCTGCTTCCACGCTCAGGAACAGGTGCTCAGATAAGGATGCTTAAGAA
+GATGGAAGGCGTTTGGGTGTGTCAGAACAATGAAGGCAAGTGAAAGACCC
+CGATTCTCTATGAGTCCCTTCACATAAACTAAAAATCTCAAAGTTACACC
+CAACAATCGCCTGTCCTTTTAAATAATAGAGGTGTAGGGGGAGATGAGAT
+ACAGCAACAGTTAACTACAGTTGGGGGCGGGATCAAGGGGAACTTTCATT
+TTCTCTATGGAACCCTTCCACGGCAAGGCAGAGAAAGATGGAGGCAAACA
+GGGCTCTTCCATGACCAGGCGTGCTTGACCTCAGAGCTGCGACTCTTCCT
+TCTTCAGCGCATTTATGGAGAGCTTGCTACACGCAGGGCCTGGAGCTGCA
+GCCTGGGAGGGCGCCCCATCTGGCGGGTAGAGTGCTTTGCCATGTCTGGC
+CCGACTTCTCTACACCCTGTTCACAACTCACCCTGCAACCTTCGTTCCCC
+GTGTGCTGCCAGCGATCCCCCTCCAGAAGCCACTCTGTCCGAGGTTCCAA
+TCACTCCCCTATTGACACCTATTCGTTCTCAGCGTTCAAAGAGTACTTCG
+ATTCCGTTGCTTTTGGGCGCAGAGACTTGAATCCAGGACCTTACACAGGC
+AAGGAATGCACGGCATTGTGAGCTACCCACACACCCTAATTGTTCCGCAG
+ATGAGGGTTCCCCCGCCCCCTGACGATTTTATCCCAGGGAGACTATGAGT
+GTGTTGGCCTCTGGCGCCAACCTGCCCCCGGATGTCAAACATCTGTTCTC
+AAACTTGGAACCTGAGCTTACTTCTTCATTCTCTGATGTTAGACAAGCCG
+TTCTTCCCAACACCACCCCAAGCGTCCCACTCCCCttttttaaaaaaaaa
+aataatCAACCAAACAACCAAACAAACCAAAAGTCTGGAGCAAAATCAGC
+ATAACTCCCGCAGGGTTGCAGAGAAGTTTACGGGCGGATTAGTGTAAACC
+GCGAGTGTAAGCCAAGTATGGTGCAAAGAGCTGTTTTGGACATGGCTTTA
+ATGAGttggtcccttttgtatatgaagaaactgaggctctcagggtaagg
+aatgttgtcctaggtctgccgttggcaagctcgggacttagcctcagttt
+ccttactgacctccTCCCCGCAGCcccgccccgtccaggccccgccccgt
+cctgcccgcgctgcagcccagctgggctcagccaatcacccgcggcgcgc
+gtcggtgagcctggcctcgcccgccccggcccggACTCCGCTCGCTCATT
+CCGCCGCCGCCGTCTGCAGACTCGGTAAGACACCGCGAGGGCAGCGCTGC
+GGCACCGCCCTGGGCTGGGCGCGCGGGTGTCATTCTTAAGAGTGTGGAGG
+GAGACCCAGACTGTGCCCGTAGGGTACGCGTGAGCCGCGCATTGGAGAAG
+CAGAGGGCACTCCCTCCCCCGCGCAGTGACGGATCTGGGGGATCCCGGGA
+CGGGAGGAAAGATGCTTGGTCCCCAGACTGGGCAAAATGCCTCCACTCGG
+GACGCGTGGGACCTCGGCTCGTGGTGTCCCGCCCCACGGTGGATTCACTC
+ACCGCGTGGGTTTGGGGTCTTCATTGCTCTGTGAAAGATGCTTATGATTA
+GGCGTGACTCCTTGGTCCCTGACCAGTAGGAGTGTCAACTCCCTTTCTGA
+CCCCTGCTCACTCCCCACTCCGCGGGTGGCTTGGGGCCAGTGTGGACGCC
+GAGCGTTCTCCAGGCTCTTTCCACCCGCTACTCTGCAGGTGGATTGGTTC
+TCGGGGTCCGTGAGGGTCGGGCTCGGCAGTAGGAAGGATGCTCGCACAGG
+GGACTTGGCAGGTGGCCGGTGCCCTCTCTTCGTGCGGGTCCCTGCAGTAT
+AGCCTTCGGGACACACCCTTGGCGCAGAGACTTAAGTGTTTTGCACCCCT
+CACCGCGGTTTTGCCCGGGGTTCAAGGGCAGGTGGGTGTCAGAGACTGCC
+CAAGGTCGCGCCGGGACCAGAGCCCGGGAGGGTGGGGGCGTCACGTGACC
+TGGCCTGAGCGAACTTGGCCTGGGACAGCCGGACAGCACGGTCTGGGCAA
+CCAGGCTGTGCGGTAACAGCGGGTACCCTTCGTTTTTCTTCATCTTATTG
+TGAATCGGGTCTGGTTTTCGTTGATGTCACAGAACACAGATGAACGCTCA
+AGTTTTTAAGGAGTTAAAAAGTTCCTAGTGTGAACCAGGCTACATACAAT
+CAAGCTCAGTACTCTCAGCTCTGGGCCGACTCTCGTTCCGTGCATTTAAA
+TAGTTGTCCAAAAACAGATTTTAGTCGGAAACTGCTAACTTTGGAAGTTC
+GCAAATAAAATGAAAGTGAGTTTAGAAGCCTTTCGGAACGCGTATTTAGT
+TACAGCATTTTGTTGCACAGGCGTCTGGTTTCTGGTCATTCCTGATATTC
+AAGCGTGTTTATCACTGTCAAAACCACAAGCCAAATGACTAAAACACAGC
+TTTGGCCTTTTATTTGTGCCAGCAAGCATACATCACCACCACCCCCTTCC
+TAGTCGGTCGACTCAGGACTCAGTGAGGACCTAAAGCAGAGGACTGTGGT
+GTGGGGAGGACAGTGCTTGCTCCGGGGCAGTGCAGAGTAGTAGGTAGGTC
+TGGGCAGCGTCCGCATTCAGAGTCCTGGGCTAGACTGGTTTTGCTGCAGC
+ACCCGGAGCTCTTTTGTCATGTAAATTATTGCTTTTCTTAACTAAAGCCT
+CGCTAGACTTAACCTTACACTTGAATTTTCTCTTTTATCTATTTATTTAC
+TTTTAAAAAAtgagataggatctcatgtaacacaggctgccctccagcct
+gctctgtacccaaggttggttttgaacccccgatctccttcctgcaccca
+cccataagtgcggtgattataggcgagcaccaccacgcccggctttGAAC
+TCCTTAACCGTCTTTGGAATCAAGCTCCGGTTAGGTTTTGTATCAAAAGT
+GGCCGAAGCGGCTTCCTGCACAAGACAAAACCTTTCGAGTTTGAGCTAGA
+AAGCCACCTGACTGCAGATGAGGGGTGGAACGCCTCCCTTCCGCCGCCGC
+TGCGCTTGGCCCTGACCCAGTGGTCACGAAACCGGCAGGCCTGATTCTCT
+CGGGAGTTTGGGGCGCTGGCCGGGGTTTAGCCAACCCTGATTCCTCTTGC
+CCATTTTGCCCATTCATAAAAGCGCTGCAATTTTTACTTTATTTTCCCCT
+TGGGTTTCGCAGCGAAACCCTTCGAGGCACGGTGCCGGCTGGCTGTTTTG
+TTGTATGCGACAGCTGTCCTCGGACAAAGCGGATCGGTGACTCCGGGATG
+GCAGCGGCGACGCGTCGCTCCGGAAGGCCTGCGTGGGCTCGGCCGGTGGA
+ACAGGATCCGAGCGCCCCGGACGCGCCAGCACGGGGGCGGGGCACCCGTA
+ACCTTTCCCCTACTTTTCTCAGCCGTCACGTGACCCGGCTGGGTAGGGGA
+AGGGGCGGGGCGGGAAGCCGCTGTTGTTAGTGCCCTTCCCTTCCCCAGCG
+CCTTGAACTTGCAGTCTGGATCTGCAGGCGGCTAGAGCCACGCGACTTTC
+CTGTACTTTGACCGTTTGAAGGTTTTTTTTTTTTTTTGGTTAGAAAATAT
+GTTTAGTCACTCTTCAGTCACTCTTCATAGATATTTACCGGTAGGCCCGA
+GTCTTAAAGCTGGTGGAAGTCTGCATTTGAACTAGTTTAGAATAAAATGG
+TAGTCCAAGGTGGATAATTTTAAAGTGTGTTTAGCAGACTGGACAGTCCC
+CTGAAGGAGGGAGAGTCGCTCGAATCTGGGAGTTAAGGGACAGCCTGGGA
+ATAGGCAAAGATCCATCCTCAGCTCGGGAAAGAAGAAAAAGGGAGGTGGG
+GTTTTAAGCCGGTGGCGGTGGCGCGCCTAGTAGGCTTAAAAAGGATTACT
+GCACACTTGAATTAATGCCAATTTAAGCTCTTAGTGCAAGAATTTTTGTT
+GTTTGGAAAATAAGCCTGCTGCCAAGCCTGACTACCCTAACTCGAAGGGT
+GAAAATGATCCCGACTTCTGCACACCGTGCTATAGTGTGCACTCAACCGC
+CACCATAAATAAATAAGATACATGGTTTTGTTTTAAGTAAAAAGCAATAC
+AAGCATATTGTGCAAAATTAGAAAGGCAAAAATGGGGTGCGATGCAGTCA
+CCTACTTACTCAGTAGTTACTGCAAAGGCCACCACTGTGAGCAGTTCATT
+CAGGACTgtgatggtgtgtacctgtaccatctagctcttcggaggtggac
+agaggagagccggacttaaggccagctaccaccatccgtgagttggagtc
+ctgtgtgggatacacaagaacttgtctctaaaccaaacCTAGACTGCAAA
+GTTTGTTTATTTTTTTAATCTCTTACCTAACACAAGGAGTGAGTTCTCCT
+TGTTGATTTCAAATATCTGTTGCCTTTTGTACTCTTCACCTTGAACCCCG
+TGCAAATATTGAGGCGGACATTGGGTCCCCACAGGCCCTGGGCTAAGGCC
+AGCTTTGCTCTGTTGAGGTAACGTGGCAGCCTGGTTCTGAGAAGTGCCCA
+CCCTTTGCCCTTTTTGTGCGAGTTGTTCTGACCTTCAGGAATGTTTTTCG
+GAAGTTAATAGCAGCAGGCACACTGCCCGTTTCGCGCCCCGACACCTGGG
+TAACTGCCACTTTAGAAGGTTGGGAAATAGGATGGCTACTGACCTTGCCT
+CTGAGGAGTGTTGCACACCGACCATTTAGGTAGAAATGTAAGAGAAGCTT
+GGTGTGGTACAAAACACTTATAATCCTAGGGTTTGGGGGATGGTGCTGAG
+GCAGGATTCCGTGACTCCATAGTGAGACCTTGACTCAAAAAACAAAATTA
+ACCAAACCAAAcccagcaaagaccggattaggctgggttgtccatgccta
+taatcccagtccttagtaggtggagacaaaattagtagttcaagatcagc
+atcagtgatgtacctggtttagggctagcatggactacataagacctgtc
+tcaaaaacaagaCAAAATACTGTATGCACTGGTATTAATGCACTGGTGAT
+ATATATTGGAGTTATGCACTGGTGCTGTGCACTGGTGTGAATGCACTGGT
+GCTGTGCACTGGTGCTGTGCACTGGTGTGAATGCACTGGTGCTGTGCACT
+GGTGTGAATGCACTGGTGCGAATGCACTGGTGCTGTGCACTGGAGTTGTG
+CACTGGTGTGAATGCACTGGTGCTGTGCACTGGTGCTGTGCACTGGTGTG
+AATGCACTGGTGCTGTGCACTGGAGTTGTGCACTGGTGTGAATGCACTGG
+TGCTGTGCACTGGTGCTGTGCACTGGTGTAAATGCACTGGTGCTGTGCAC
+TGGTGTGAATGCACTGGTGTGAATGCACTGGTGCTGTGCACTGgtgctgt
+gcactggtgtaaatgtactggtgctgtgcactggtgctgtgcactggtgt
+aaatgcactggtgctgtgcactggtgctgtgcactggtgtgaatgcactg
+gtgctgtgcactggtgtgaatgcactggtgtgaatgcactggtgctgtgc
+actggtgctgtgcactggtgtgAATGCACTGGTGTGAATGCACTGGTGCT
+GTGCACTGGTGTGAATGCACTGGTGCTGTGCACTGGTGCTGTGCACTGGT
+GTGAATGCACTGGTGCTGTGCACTGGTGTGAATGCACTGGTGTGAATGCA
+CTGGTGCTGTGCACTGGTGCTGTGCACTGGTGTGAATGCACTGGTGTGAA
+TGCACTGGTGCTGTGCACTGGTGTGAATGCACTGGTGCTGTGCACTGGAG
+TTGTGCACTGGCTGTGGCACTTAGGAAAACAAAGGTCATCTATACTCTTT
+CTGTCTCCTCCTCCTCCATGTGTGGTCCAAGGAGCTGAGTCTCACTTCTG
+TTTCTTAAGTCCCACTAGAATTTGTCTTCCTCAGTCTCCCTGACCCTATG
+CAGGCCTGCAAATCATTGCTGAAGGAAGGACAGGTTTGGGGCGCCCTTTC
+TCCGCTGGACTGAACCAGCCTACTGATATTAAGGGGGTGAGGGCCTTTTG
+GAAGTTTCACTGGCTACACCCCTAGAAATTAATGCCCGAGAGGGAGGGCT
+TAGAGGAAGTGGTTGGGCCCCTAGCTCAGTGTGCTTCCATGGTACGTGGC
+TCTGGGATGACTTGCCTGACATCTCTGTCCCCATCCAGGCCACATGCTCT
+CTGCAGTGACCACGTCCACACCCACCTCTCTTCTTTTAGGGTTTCCTTGG
+CTTTGGGTAAAGCCATGAAAAGAGAATTCAACAAGCCTCGTTATCATGGC
+CTGAAGGGATATTCGTATGTCTACAGGACAGGGACACTGAGTAACTCCCC
+ACAACCCTATCCCCCTtgtagtcctggctagcctgaaactcactatgtag
+accaggatgactttgaacttgtgatcctcttgctccacttcAGATAAAAA
+CTTGGCCCTTTATGAAACTGGCTGGTTTATTAACATACTCACCCCTAGCT
+TCCAGCAGCTGCTCCTGGAAATGCTACAAGGAAGGTCCAGCCCCGGAGCC
+CATTGCGTCCTGCGGGCCTGTGAAGGTATTCTGAAAAGATATGAATGAGC
+TGCCCATGTTAGTCAGTTAGAAGATAGGCTGAGGTACCATATGCTCGCCC
+TGAAGCATTGAGCTGGGTGGGCCTTGGGGGATAGAGCCAGGACAGACACC
+CACTTTCTTGAAGGACAGGTGTTGACTGCTCAGGCTCCTGGTGGGATAAC
+AGAGTGTGGCCTTGTATTAAAGAACACGTTCTGTGTTTGCACACTCTAGT
+ATCCTTCGATTGATGGGAGCTGAGGCAGTCTGTTCTGCCCTGTGCTGATA
+AAGCATAGGAGAGAGGCTGATGTTTGTCAGTGAGCTGCAGATCTGGAAGT
+GAACCCAGATCTGTGTTGTAGCCACTCTCTCACCTGCTGTCATAGAGCAG
+GGCTCTTAGTGGCAGCCATCACCTCTATATATGCAGACTTAGACTGATAT
+CGAAGTGCGGGCATGTCTGGGTGTTCATTTCCTTCTCTGTCAAATGGCAG
+CTCTGATACCTGCTCTCCTGTGTCCCTTGAGTCCCAGGAGACTCCATTAA
+GGAGTGAGAcctcagtcttagcattcaggtgacaaagataggctgatctc
+taggtttgaggctggctttgtctTCCCGCAGTATGACCTATGCAAAATCG
+TGAACTTTATATAAAAAAAGGATTTATTTTATTCATCttttttgtttttt
+gttttttgttctttgttttgttttaggatcgctatgtatatagcctttac
+tagcctggaacttgctacatagaccaggctagtcttgaactcacagatat
+ctacctgtctctcgctccagagtgctgggattaaagtgtaccaccacaca
+cagTGCTTTTTACATTTTTAACTTTTTTATTTACGAGTATGCTATGCATC
+TCCGTGTGCGCACCTCCGATGGCTGGGGGCATCAGCTCCCCAGGGGCTGG
+AGACAGGCAGTTATAAGCTGCAGAGGCACTAGGAGCTGTGCTCACTCCTC
+TGAAGAGCCTCAGGCACTCTTAGCCTCCCTCTAGCCTGGTCCCtgatgcc
+tgaaaacaccacacatcccatggaaagtgaatttagaaggttgactttgg
+atcttctcctggggctaatgaggtgaagtgccatcttccatgtgagtctg
+ggtgacttcagcatgacccacaactGTGAGGAGGACCAGAAGCCCTTCAC
+AGGACATTATGTTGTTAAGGTGTGAAGGTGTGACAGACAAGCAGTAGATT
+GAATGGACTCCGTGCTTTTTCCTTTTTTTTTTCCCACTGCATGGAGACTG
+GCTATGAGGATTATTGACGAActtgtgcaagcagcagacattcttaagcc
+ctaagccatgtctccagccccACCTAACAGCATTTTCTACCTGGAGGTGG
+CCTGTGGCATGTGACCCCTGCCCCACACATCAAAACATTTGTAGATACAG
+GTTCTAGACGCCAGTGTCAGGACTGCACCCGGGCGGGTTTTCTGGTGGTC
+AGATCTCAGGTTGCTGAGGTGACAAACATAGACAGGATGTTTAGAACAGT
+CCCTGAGGATTTGGGAACGTGTATAGGGACAGTGGTATGAGGAGAAGTTC
+AGTTTTCTTGAGCTAACAGATTCATGCCACTTCCTGGCAGTCAAGAGTTC
+AGGCTGGCATCCTGTTCTGGCAAGATTGGACCCATGTGCTGTTTCAGAAT
+GGATGGGGTAGACTGTTAGCCTTGTTAAAGTGTATTTCACGTCTTATTAC
+AAATTTTTACATGTTttgttgttgttgttgttgttgttTTGGTATTGTGA
+GGCAGAGgtgtgtgtgtgtgtgtgacctgtggggaggtcagaggacagtt
+tgtgggacttggttctcttcctctcctgtgcgggtctcttgaagattgaa
+ctcagttgacttggcagcaagagccttctcctgctgaatcatgttgctgg
+tccTCTTTGTTACTTTGTTTTGCAGtttttgagacagagtcttagatatg
+cttggtgagcttgaactcactatgtagttgaggacaatctgatcctcctg
+cctccccctcttgagtactgggattacaggtctgtgccaccaagcctgct
+ttagtggtgttagagatgcagggtcattcggacttaccccatgctagaca
+agcactctgtcaactaagccatgtccccagtcGTGGCTACTTCCCTTAGA
+AGTGTGTCCTCTGCTGGCTTCCCCATGTGTCACATTTCTCTGATTGCCAT
+TTCTTAATGATGTGCTGCAGTCGCCTAAATTGGAttttgctttactttga
+acttttctttactaagtagctctagctggcttagaactggagatgtagac
+caggctggccccaaatgtacagcagtccctctgcctgctcggattacggg
+caagctccaccacacccggctTTTATTTCATTATTATTGTTATCATTTTA
+AATGgaggcagggtctctgtagcctcagctggctttatggccacagagcc
+tttgcattcctgattctgttgtcttcagctcccaagtgctggAGCTGGAA
+CGATTCGGCATCCTGTCTAGCATGGGTTTTTACAGTGTGTGGTAGGCGGG
+ACTTCTCTTGTTATTTTGGGGGAATGTAGACTGAATTGAAAATAGATTAA
+AAAAAAAAAAGAAAATAGATGGAAATCTTACTTTTACCATCCAAAAACTA
+ACCCTGCTTAGCTTCTTTTAAAAATCAGACCATTTAAAATGGTATGGCCA
+gggctggagagatggctcagcggttaagagccgactgctcttccaaaggt
+cctgagttcaattcctagcaaccacatggtggctcacaaccacctgtaat
+gggatccaatgccctcttctggtgtgtctgaagacagcaaactatgtact
+cacatatgtaaaataaataaataaatcttttttaaaaaaTTAATAATAAA
+ATAGAATGATATGGCCATAGACCAGAATTTGTTTTCTAACCTGATCTGAA
+CTATTGTGTTCAGCCAAACAGCACAAATGGCTTATGGTGATATGCCATGA
+TGTGGGAAAGTCACCTAGGGCTAAATTACATAATGCAAATGAAGACTGTT
+CAGGCATGAATTCCAAATTTAACCTTTCAGGGTGAGTTCCTGTGACCTCT
+CCACCTATACAGTAAGTTAACAACAACAAATTGAAATCTGGTAGCCAATG
+TGACAGTTTCCAAGGTGGAGTCTTTCAAGCAGGGTCTAGTGTCTTGGTCT
+GGATTCGTTCTTAGATTGGATTAATTCTCATAGGTACAGTGCCTTGGGCC
+TGCTTTCTCTCCTCCACACTCTTCCACTCTTGCCCACGCTCCAACCCCTC
+CAGTGCCTTCTCCCATCCCAGGACATAGCATAAGGCTCTCACCGAGAAGG
+AGtgatcctgaactctccagtctctggagctatgagacccataactctct
+ttataaagtacccacccttggcaactctgttacagcaactgtaaatctac
+taagacaTTCCTTCACCTTCCTCATACCCCAAGCCAGCCCACAGAAGGCA
+CAAGGTGCAAAGGTCTCATTTCTATTTGGGTATAGCAGTTGTACTCAGAT
+TTTTAAGTCTCTTTTTTATTTTTGATGTGTGCGCATTTCACATGTGTATG
+TAGCCCAGAGGCCACAGGCAGTGTCATCTGCAGTTACTCTTCGGCTTTCT
+TTTTTTTTTCTTTGAAAGGAAGGTTACCCCTACCAAGTCTTTCTTGTTTA
+TTTTAGATTTGAAGTGATTTACAGAACTTAGATATAAGGCTTTGAAACCT
+TTCTTTCATCCTAGAGAAGCTCACATGTATTTGtctttttaaaaatattt
+ttattaggtattttcctcatttacatttccaatgctatcccaaaagtccc
+ccataccctcccccccccactcccctccccacccactccccctttttggc
+cctggcattcccctgtactgtggcatataaagtttgcaagtccaatgggc
+ctctctttccagtgatggctgactaggccatcttttgatacatatgcagc
+tagagacatgagctctggggtactggttagttcataatgttgttccacct
+atagggttgcagatcactttagctccttgggtactttgtctagctcctcc
+attgggggtcctgtgatccatccaatagTATttttttttctttgaaacag
+gagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtaatggccttggcta
+acgtggacttatttattgaccaggctggcctcgaactcacagagctccac
+ctgcctctggctcttgagtggtatgctcgaccatgcccagcctctctaag
+ttacagccatttctgtTTAGCGGAGCAGAGCGCTCCCAGAAGTTAGATCC
+CAGCAGCAGCATCTGTCCAGGGGCAAGGCCCAGGGTTCATCAGCCTGGTG
+CTGTTCCTTGTGAGGGATGCCTGCCATGTTCCTGGATGTCCTGCCTAGAA
+TTCTGTTAAGGTGCCACTTCCTGTGGGTAACCCTTTCTCTCAGGATTTCC
+AGAGGTTGTTTACTGCTAGTCAAGATGGACAGCTGGTGAGGGATTAGAGC
+TGCAGGCAGAGCCTGTGTCTGCCTGGCAATGAATGATGTGATTCTGGTGG
+GCACCTAGGTCACACTGATAAGAGTCATTAGCCTTGGTCCGAGTTTGTAG
+TAATCAAGTTTTCCTGTTGGCTACCATCTATCATTTTGGCTACAGCAGTG
+ACGTAAGCTGGTGTGTGTTGCAACTGCAGGAATCTTTTGCTAGCCTTTGC
+TGTCACAGCTGCTACTGCACTTTGGAAGGtaaggacatgcccactggagc
+tgagcctggacctgattcctgctttacagttggctagctatgaccttacg
+caagcgtttgacatctgagtcttgttttcctcgtcagtgaatggggacaa
+ccggggattcattaattagagttgtagttagaatttaacaagctgatgga
+tgagaaacaaattaataataataataaaaCCGGCAggtggcccatgccct
+taattccacttggtaagcagaaggtggaatctgtgagtctcaggccaggc
+agggcctccctcatagaccctgtcagaagaagaagaGAAAAGGCTTggga
+tgaggatacggttcggtgagttatgtgcttgccgtgcaagcatgaggagc
+tgagtacggatcccagggcccacataagaagccgggagcagtggtgcata
+tctgtaatgctaaccctgggattagagacagagaccggaggaaccctggg
+gctcgctggttagccagcctccccacatcggcggtctctgggctccgagg
diff -r 000000000000 -r 87f7630ab82f test-data/test.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/test.bed Thu Sep 25 14:05:16 2014 -0400
@@ -0,0 +1,6 @@
+track name="MACS peaks for MACS_in_Galaxy"
+chr19 108 504 MACS_peak_8953 185.56
+chr19 3876 4233 MACS_peak_8954 145.91
+chr19 3345 5762 MACS_peak_8955 204.10
+chr19 6337 6943 MACS_peak_8956 333.21
+chr19 13013 13650 MACS_peak_8957 165.69
diff -r 000000000000 -r 87f7630ab82f tool-data/all_fasta.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/all_fasta.loc.sample Thu Sep 25 14:05:16 2014 -0400
@@ -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):
+#
+#
+#
+#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 000000000000 -r 87f7630ab82f tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Sep 25 14:05:16 2014 -0400
@@ -0,0 +1,7 @@
+
+
+
+ value, dbkey, name, path
+
+
+
diff -r 000000000000 -r 87f7630ab82f tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Sep 25 14:05:16 2014 -0400
@@ -0,0 +1,9 @@
+
+
+
+
+
+
+
+
+