Mercurial > repos > jjohnson > cistrome_misp

--- /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 @@
+<tool name="MISP: Motif-based Interval Screener with PSSM" id="misp" version="0.1.0">
+  <description>Input one or more motifs, find all hits in peak regions</description>
+  <requirements>
+    <requirement type="package" version="2013-11-28">misp</requirement>
+    <requirement type="package" version="2.19.1">bedtools</requirement>
+  </requirements>
+  <command>
+#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 &amp;&amp;
+misp out.fasta $motif_db $pvalue $motif_id output &amp;> $log  &amp;&amp;
+cat output* > $outputtxt
+  </command>
+  <stdio>
+    <exit_code range="1:" level="fatal" description="Error" />
+  </stdio>
+  <inputs>
+     <param format="bed" name="bedfile" type="data" label="bed file for regions">
+       <validator type="unspecified_build" />
+     </param>
+    <conditional name="refGenomeSource">
+      <param name="genomeSource" type="select" label="Use a built in reference genome or own from your history" help="Built-ins genomes were created using default options">
+        <option value="cached" selected="True">Use a built-in genome</option>
+        <option value="history">Use a genome from history</option>
+      </param>
+      <when value="cached">
+        <param name="index" type="select" label="Select a reference genome" help="If your genome of interest is not listed, contact the Galaxy team">
+          <options from_data_table="all_fasta">
+            <filter type="data_meta" ref="bedfile" key="dbkey" column="1" multiple="True" separator="," />
+            <validator type="no_options" message="No reference build available for selected input" />
+          </options>
+        </param>
+      </when>
+      <when value="history">
+        <param name="ownFile" type="data" format="fasta" metadata_name="dbkey" label="Select the reference genome" />
+      </when>  <!-- history -->
+    </conditional>  <!-- refGenomeSource -->
+     <conditional name="motifopt">
+       <param name="motifopt_select" type="select" label="upload a motif or select from our database.">
+         <option value="upload">Use uploaded motif</option>
+         <option value="database">Use motif in cistrome database.</option>
+       </param>
+       <when value="upload">
+         <param name="motif_file" type="data" label="motif file" />
+         <param name="motif_id" type="text" label="The motif id in uploaded motif file. Or write 'all' to run all motifs in the file." />
+       </when>
+       <when value="database">
+         <param name="motif_id" type="text" label="The motif id in Cistrome motif collection. Or write 'all' to run all motifs in the file." />
+       </when>
+     </conditional>
+     <param name="pvalue" type="float" label="p-value cutoff for the motif screen" value="0.001">
+      	<validator type="in_range" max="1" min="0" message="pvalue is out of range, width has to be between 0 to 1" />
+     </param>
+  </inputs>
+  <outputs>
+     <data format="txt" name="outputtxt" label="MISP hits on ${bedfile.name}"/>
+     <data format="txt" name="log" label="Log of MISP on ${bedfile.name}"/>
+  </outputs>
+  <tests>
+    <test>
+      <param name="bedfile" type="bed" value="test.bed" dbkey="mm9"/>
+      <param name="genomeSource" value="history" />
+      <param name="ownFile" type="fasta" value="mm9_chr19_part.fasta" dbkey="mm9"/>
+      <param name="motifopt_select" value="upload" />
+      <param name="motif_file" value="misp_motif" />
+      <param name="motif_id" value="M00139" />
+      <param name="pvalue" value="0.001" />
+      <output name="outputtxt" file="misp.hits"/>
+      <output name="log" file="misp.log"/>
+    </test>
+  </tests>
+  <help>
+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
+
+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
+  </help>
+
+</tool>
--- /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	*
--- /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
--- /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
--- /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
--- /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
--- /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):
+#
+#<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.
+#
--- /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 @@
+<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>
--- /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 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  <package name="misp" version="2013-11-28">
+      <repository changeset_revision="ee7a28372e5e" name="package_misp_2013_11_28" owner="jjohnson" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bedtools" version="2.19.1">
+      <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+</tool_dependency>