# HG changeset patch
# User bgruening
# Date 1497356706 14400
# Node ID 222b7f7b8432845e28f86e54e14d22343486956b
# Parent  db0f5c1cb22750a6dccb7d06563fe90f687028a3
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/crt commit 4241c1d4b05a177bd2c74f5a139f51d4f65e0b55

diff -r db0f5c1cb227 -r 222b7f7b8432 crt.xml
--- a/crt.xml	Fri May 02 06:15:38 2014 -0400
+++ b/crt.xml	Tue Jun 13 08:25:06 2017 -0400
@@ -1,17 +1,18 @@
 <tool id="crispr_recognition_tool" name="CRISPR Recognition Tool" version="1.2.0">
     <description>(CRT)</description>
+    <!-- split_size needs to be 1, because CRT does not support multi fasta file -->
     <parallelism method="multi" split_inputs="input" split_mode="to_size" split_size="1" merge_outputs="output,output_region" />
     <requirements>
         <requirement type="package" version="1.2">crisper_recognition_tool</requirement>
-        <requirement type="set_environment">CRISPR_RECOGNITION_TOOL_SCRIPT_PATH</requirement>
     </requirements>
     <stdio>
         <exit_code range=":-1" level="fatal" />
         <exit_code range="1:" level="fatal" />
     </stdio>
     <command>
+<![CDATA[
         temp_output=\$(mktemp);
-        java -cp \$CRISPR_RECOGNITION_TOOL_JAR_PATH/CRT1.2-CLI.jar crt
+        crt crt
             -minNR $minNR
             -minRL $minRL
             -maxRL $maxRL
@@ -24,17 +25,18 @@
             \$temp_output
             ;
 
-            python \$CRISPR_RECOGNITION_TOOL_SCRIPT_PATH/reformat.py \$temp_output $output_region $output
+            python $__tool_directory__/reformat.py \$temp_output $output_region $output
+]]>
     </command>
     <inputs>
         <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/>
 
-        <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/>
-        <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region"/>
-        <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region"/>
-        <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region"/>
-        <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region"/>
-        <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs">
+        <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have" help="-minNR, default 3"/>
+        <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region" help="-minRL, default 19"/>
+        <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region" help="-maxRL, default 38"/>
+        <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region, -minSL, default 19"/>
+        <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region, -maxSL, default 48"/>
+        <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs" help="-searchWL">
             <option value="none" selected="true">default</option>
             <option value="6">6</option>
             <option value="7">7</option>
@@ -60,15 +62,20 @@
         </test>
     </tests>
     <help>
-CRISPR Recognition Tool - a tool for automatic detection of clustered regularly interspaced palindromic repeats
+<![CDATA[
+
+**What it does**
 
-http://www.room220.com/crt/
+`CRISPR Recognition Tool <http://www.room220.com/crt/>`_ is a tool for automatic detection of clustered regularly interspaced palindromic repeats (CRISPR). It rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes. 
+
+**Input**
 
-**Citation**
+DNA sequence in FASTA format
 
-For the underlying tool, please cite `Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P:
-CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209`
-
+]]>
     </help>
+    <citations>
+        <citation type="doi">10.1186/1471-2105-8-209</citation>
+    </citations>
 </tool>
 
diff -r db0f5c1cb227 -r 222b7f7b8432 test-data/crt.tab
--- a/test-data/crt.tab	Fri May 02 06:15:38 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,142 +0,0 @@
-CRISPRs	1	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GATTGTTGTGCCCCTGGCGGTCGCTTTCAATGCCT	37	35
-CRISPRs	73	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TAATCCTAATTAGGTTTGAGTTAGTATCTAGTGCCAT	37	37
-CRISPRs	147	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ACAGATTTTGCTTCAGCTAGTACCAAAGGCTAG	37	33
-CRISPRs	217	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCGTAACTACCTTCTAAGTCTGTAGCGATGAATGTGG	37	37
-CRISPRs	291	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CAAAATATAGGGAAGAATTTTAGAAAGAACCTCAGAA	37	37
-CRISPRs	365	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AACTAAGGCATCCCATAGCATTCCGCTACGATCTATCAG	37	39
-CRISPRs	441	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TAATAATTGCTGATTAATCGTGGTGGTGGTGGTGG	37	35
-CRISPRs	513	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GATATATGGCTAAATATTGCTCAAAAGATTTTAATA	37	36
-CRISPRs	586	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATTAGATTGGTCGTGTTTTGATTAACGGTGCTAGC	37	35
-CRISPRs	658	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTGCCATCCCAGGCAACATAGCAAGCATGGAGGTG	37	35
-CRISPRs	730	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTGCCATCCCAGGCAACATAGCAAGCATGGAGGTG	37	35
-CRISPRs	802	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTGCGGACAGACTCGATTAAGTCAATAACAGCTTGG	37	36
-CRISPRs	875	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CTTGCCCTAATTTTCCTGGTGGAAAAGCCGCTGGCT	37	36
-CRISPRs	948	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATAGCAAGTTGCTAGAGAAAGCGCAACAAAACAAG	37	35
-CRISPRs	1020	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GAGGTTAAATTGTTGTCGATTCAAGAAGACTTGA	37	34
-CRISPRs	1091	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AATAGACACGAATTCCGGTTCCAGACCCAGCCCGTT	37	36
-CRISPRs	1164	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTCTTCCATCAGTCCAAGTTCTTCAACAATGTCTA	37	35
-CRISPRs	1236	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TGCTGAAGAAGCTGGAGAGAATCGGGCATCGCTAT	37	35
-CRISPRs	1308	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATTCCAGATGTGGTGGAAGAAACCTACGCCCCCGA	37	35
-CRISPRs	1380	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AATCAGCTTCCGGCGTTGCCATTTGGATTCAA	37	32
-CRISPRs	1449	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GTGAGGGGGCCAGATCCCTGCCAGATCCCCCAAT	37	34
-CRISPRs	1520	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATTAGATCTTTGGCATAAGGCAACCGAAACTGATC	37	35
-CRISPRs	1592	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GATTATCGTGCTTCCTTCGATGCTAACTTTGCTCT	37	35
-CRISPRs	1664	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCCATAATGATTCTGCCTCGTTTCTACTTGGTTTA	37	35
-CRISPRs	1736	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TGTATGTCACGCCATCGGACAGGTAGGGAAAGCCTGG	37	37
-CRISPRs	1810	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CAACTGGCTAAGCTGGTCATAAGGCTTTGGGAATGAAA	37	38
-CRISPRs	1885	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCGGGTTTCCCTCCTGGGTAATGACGCCTACGGG	37	34
-CRISPRs	1956	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CAAAGCTGGCACGGAAGCCCTTAAGGATATCCTC	37	34
-CRISPRs	2027	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GATGCAGAGATTCCACCACCAAAGGAGAATCCGATAA	37	37
-CRISPRs	2101	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAG	37	37
-CRISPRs	2175	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGG	37	41
-CRISPRs	2253	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAG	37	37
-CRISPRs	2327	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGG	37	41
-CRISPRs	2405	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AAGTAAGGTTCAAACGCCGCTACGCAGTCTGGTCC	37	35
-CRISPRs	2477	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CAAAGTTGGAACGAAAGCTAACGACAAAAACTA	37	33
-CRISPRs	2547	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTTAGCCATCGTCGGATTCTAATCGATCCAAAAGTCGG	37	38
-CRISPRs	2622	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AATCCTACCAAGCGGCTTTTGGTGGGCCTGGCTCCGA	37	37
-CRISPRs	2696	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTCGGTTGATTGATGAAGATCTGATCGTCGAGTGGT	37	36
-CRISPRs	2769	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCCCTTTTCGGGGATAGGTGGTGTCCCTTTTCGG	37	34
-CRISPRs	2840	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ACTACCAGGGGGAAATTGATGGTATTCCCGGCAAA	37	35
-CRISPRs	2912	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ACTACCAGGGGGAAATTGATGGTATTCCCGGCAAA	37	35
-CRISPRs	2984	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GGGCAATGTTAAGCATGGCTAGAAGGAATAGTTAAC	37	36
-CRISPRs	3057	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTCCATTAATGATTCTTCAAAAATCACTCGATT	37	33
-CRISPRs	3127	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ACTGTTACTAGCCACCGCCCAACTCCTTTAATACTT	37	36
-CRISPRs	3200	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCTTCTGTTACGTAGATTTTTCCTGTTTCGCCAACAG	37	37
-CRISPRs	3274	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CATCGCTCCCAGCATATTGTCCTGAACGGTCGGCAAT	37	37
-CRISPRs	3348	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GATTTTTCCAGTGATGGTGCATACCTAGCCGTAG	37	34
-CRISPRs	3419	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TAGTCCCTCCCACACTGCCAATATTTCTTCAT	37	32
-CRISPRs	3488	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCCGTCTGTATGACTTATACTCGCAAGGATT	37	31
-CRISPRs	3725	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGTAGTAGAACCAATCGGGGTCGTCAATAACTCCCG	37	36
-CRISPRs	3798	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGGGGCTTGGGGGGTTGGAGTCCCCGCCCCCGTGGTGGGA	37	40
-CRISPRs	3875	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGTGAGTTGCATAATGCCTCCTAATGGCTGTTGGACTCATAA	37	42
-CRISPRs	3954	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTTGGTATTTGTAGTTCTCGATGAGTGTTTTAGGCA	37	36
-CRISPRs	4027	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGATAACGGGATGCCAGCCCTAAAGGTGATGAGCGG	37	36
-CRISPRs	4100	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGTTATCCGGCAAAGAAACCACACTACTAAGCTCGACAA	37	39
-CRISPRs	4176	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGGGCCGGGCGCGAGTTGTCCTCCTGTCCGAGGCCCCAC	37	39
-CRISPRs	4252	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGTTATCCGGCAAAGAAACCACACTACTAAGCTCGACAA	37	39
-CRISPRs	4328	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGGGCCGGGCGCGAGTTGTCCTCCTGTCCGAGGCCCCAC	37	39
-CRISPRs	4404	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTATTAAGGCTATTTTCGCCACTTCTGTTTGAAAG	37	35
-CRISPRs	4476	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GTCACACCTCTTCACGAATCCTCACATCATGAATAAGCTGCACA	37	44
-CRISPRs	4557	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGCGGGTCGAGATGTCGCTGGACACGCTGGTGCCGGACA	37	39
-CRISPRs	4633	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTGGGCGGACTGGAGTTGCCACCTGCCGATGGCCTGCA	37	38
-CRISPRs	4708	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GAGCCAAAGTCAACTAGCACAGGCACGGCAAGCCATCCTGA	37	41
-CRISPRs	4786	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TCGTGCATCTGCGCATAGGAAGAGGTTAATTCCTCAAC	37	38
-CRISPRs	4861	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AACGGGCAGCCCGAGTGGTGGGCATCGAGGTGGTGCTC	37	38
-CRISPRs	4936	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CCCCGCCACATTTTCGGATTAGAGGATTTGAATCGGCCGT	37	40
-CRISPRs	5013	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AGTTTCTCAAACTTTTCGGCGATCGCCGTCCAGGTGAGTTGA	37	42
-CRISPRs	5092	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TAGCGAAAAGTTATAGTTACCTTTGACCGGAGCTACCAACTCA	37	43
-CRISPRs	5172	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CCCCGCTGCCACGAGGGCAGCTGTAGACGCACCCC	37	35
-CRISPRs	5244	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TTAAATATACCCATCCCTAATAAAGGATAGAGATCTTGCA	37	40
-CRISPRs	5321	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GCTCTATTCTAATAACCCAAGCTTTTTTCAATTCTAA	37	37
-CRISPRs	5395	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CCGCTTGGTAGGATTGACCACCAAAGCTAGAAACAGGCACA	37	41
-CRISPRs	5473	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AGGGCGGTTAATCACTAGCGGCGATCTAGATATTG	37	35
-CRISPRs	5545	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TAGACTTCTATTTCCCCTCTTGCCGAGGGATGATACTGCAATTGA	37	45
-CRISPRs	5627	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGCGCTCTCTTATCAAACGCCGCAACGCCATCAAGGCT	37	38
-CRISPRs	5702	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	ACGAGCGGAATCTTCTATGGATCGGATCACATCCTTAAT	37	39
-CRISPRs	5778	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTGGTGTCGGGGTTGTAGTATTCGTCTCGGTACAACA	37	37
-CRISPRs	5852	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	ACTATAGGGAGCGTTACCCTAGCTAGACATTGCCTAATCT	37	40
-CRISPRs	5929	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AAGAAGCAGAATAATGCGATTGAGTGGACAAAAATAAGAA	37	40
-CRISPRs	6006	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GGTTACGTATCGGCGTAACCGCCACTCCTTAGAG	37	34
-CRISPRs	6077	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGCCTCCTGCGCCCTGGAGGGGTGATCCTACACCTCGCG	37	39
-CRISPRs	6153	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GATTCTGGTATACGTTTATCCCACCACTCCTTAGCT	37	36
-CRISPRs	6226	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTCGTAAGCTAGGCAACGGCCTTGCTCGATGCACA	37	35
-CRISPRs	6298	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GGTGCAGCTGCGCCTAAGGAGATGGCTGTACAAGCT	37	36
-CRISPRs	6371	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CACCTAGAGGGTACCTCCCGGTTAGACCGGGGCTCTTAT	37	39
-CRISPRs	6447	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AACATGGCCACAACAACCTTCCCGGAGCAAGGGATG	37	36
-CRISPRs	6520	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GGCGATATTTGGCGTGCCAGCCAAGTGAATTTTGGCGCTG	37	40
-CRISPRs	6597	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AACATGGCCACAACAACCTTCCCGGAGCAAGGGATG	37	36
-CRISPRs	6670	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GGCGATATTTGGCGTGCCAGCCAAGTGAATTTTGGCGCTG	37	40
-CRISPRs	6747	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTAGCCTTTGTGGCTAACCCTCCTGCGCTTTGACATATAG	37	40
-CRISPRs	6824	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TTTTACCTCTTGCTCCTGCACAAGCTCAGCCTTAA	37	35
-CRISPRs	6896	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TCCTCCTCGCCTCTGAGAAAGAGTATGAAACACTGT	37	36
-CRISPRs	6969	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	ATGAACAGATTGCCATCTTCTAGGCGGATAGCCTGGG	37	37
-CRISPRs	7043	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGCCCATTGTTTGTGCTTCCGGAAGAAGTCTTTCAACTTC	37	40
-CRISPRs	7120	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GTTATCACGAGTTATCTTGCGCAAATCTTGTAGTGCATCTTTT	37	43
-CRISPRs	7200	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TTTAGCGGAGGAGACCTCTTCTATTTCTCCTATAACC	37	37
-CRISPRs	7274	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GGGAGAACCCTAAAAAGTTCTCCTGTCTAATCGCCACCTGT	37	41
-CRISPRs	7352	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGCTCCAGAGTGCGCCGCCGCCGAATTGCGGTCCA	37	35
-CRISPRs	7424	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GAGACTCTATCTTTGGAGTTTCTAAGACATTGGCGGTTTCTAGGG	37	45
-CRISPRs	7506	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	ATTGCTTGGCGTAGGTTGACTTACCCGAGCCTGGGAGACCA	37	41
-CRISPRs	7584	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TCCAAGGGCTCTTCGTCTTCAAAGGCCTTAGTTACCTCTG	37	40
-CRISPRs	7661	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	ATAATAAAGCACCCTCAACGGACTATGCCATGAACAACAGGACCC	37	45
-CRISPRs	7743	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GTTGCCAGTTTTGCCGTTTTTGCTGTTCTGAGAT	37	34
-CRISPRs	7814	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CCCATAATAATTAGGCTCGCTACCATAAGGGGAAACTTCTTCCAAG	37	46
-CRISPRs	7945	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTTTAGGTGGGCGTTGACCTTTAGATTAGGAATGGT	35	37
-CRISPRs	8017	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAGCGCCACAGCTGACAGAGTTCCTGAAGGAAGCTAA	35	37
-CRISPRs	8089	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTGAGTGATTTTTATCAATTGTCGAGCTTAGTAGT	35	36
-CRISPRs	8160	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CACAGGAGTGTTAGCGCACTGCCTGTCATTACTATTA	35	37
-CRISPRs	8232	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTTAGATTGCGGGGGCTAGTGACGCCATAGTTTAACGACA	35	40
-CRISPRs	8307	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAAAGATATTAGGCTATCCTTCGGGGTAGTCTTTCTT	35	37
-CRISPRs	8379	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAAGTGTTGTTGCCTAGTGTTATACCAGAATATCCC	35	36
-CRISPRs	8450	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTCATTAGTGCTATCTTCTTGTTGATGGATTAGAACA	35	38
-CRISPRs	8523	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTCTACTCTGGTGAAGACCAAGTGGATTTCGTGGTGAT	35	38
-CRISPRs	8596	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CGTTAGTGCTTGGTTGTGGTTATGCTGCAACTAAGCC	35	37
-CRISPRs	8668	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CATCGATATACTTTTTAGCATCAGCTAAATGATAAAAA	35	38
-CRISPRs	8741	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTTAGAAAGTTTTGGTTAGTTTCCATTCCTCTTTTT	35	36
-CRISPRs	8812	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTTTCTCCATTGTTAGTTAGTCATTTCCTTGACAATT	35	37
-CRISPRs	8884	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTGGGATTCATGAACATGTTGATGGTGAATTATACCT	35	37
-CRISPRs	8956	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTGATTAAATTAATATGCGTGATAGATTAACTCATTTTGGTT	35	42
-CRISPRs	9033	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTTTTTTGGCATAACTCAGTAAGTCTTTTTTGTTTA	35	36
-CRISPRs	9104	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAATACTAATCTTAAAGATCTTGGTTTAATTACATATCGT	35	40
-CRISPRs	9179	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAACAATTGCAAGGTTTATAAGTAAATGAACAACAACG	35	38
-CRISPRs	9252	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAAATCCAACAACTTCTCCACATTTACTCCACTAGTCTC	35	39
-CRISPRs	9326	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTCCTACTTGTGCAGCCTCTAGTCCGCTTTTTAGATTGCG	35	41
-CRISPRs	9402	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CGCTTCGCTTCTTTCGCTTTCTCAACATAAAACTCATGAT	35	40
-CRISPRs	9477	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTAAAGTATGGTAACTCTGGGTAATTTTTTAACAG	35	36
-CRISPRs	9548	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTTATCTTTTTCTAGCGTAACAAAAGAATAATCAGGA	35	38
-CRISPRs	9621	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTTTCAACCAAAAGCTTATTGGCTTCTACGGACTCACGAGC	35	41
-CRISPRs	9697	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTCTGAACTACTTTTTTTTCAACGACTTCACCATGGGAAG	35	40
-CRISPRs	9772	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAGTTTTAGATGCACCAATTACATCTTCTTCCATAAAGGA	35	40
-CRISPRs	9847	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CATTCAAGACCTCCGGTGGTCAGAAGACTGTAGCAACAAAGCTTGAG	35	47
-CRISPRs	9929	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTAGATCAGGCATCCAAACTCTTGGGCGATGTCGCGTAAC	35	40
-CRISPRs	10004	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCGATGTAGCTCATAGCGACCTCGATAATTAATTGAT	35	37
-CRISPRs	10076	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CACCAAGCTAGTCACTATCCGATCAACCGTCGTTGCAGGT	35	40
-CRISPRs	10151	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTATCAAGAGTTGTCTAGTCAGTTCCAAGAAAAACCCTGGGAG	35	43
-CRISPRs	10229	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTGACCTGATTCCTCGAGAATTGAGACTCCTAAAGAAATTGC	35	42
-CRISPRs	10306	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAGTTCCAGTCGTGCTCCAAGGGCTCTTCGTCTTCA	35	36
-CRISPRs	10377	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAACTTTGGAAAATTGCCTTCATACCATTCTTTTGTTAAACCGTTGTT	35	48
-CRISPRs	10460	GTCTCCACTCGCAGGAGAAATTAATTGATTGGAAA	CAGCAACAAAACAGCCAGCAGCAATTAATAAATCAGTT	35	38
-CRISPRs	10533	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CACTCCGTGGCGTCGTACCGGTACGCCTGGGCTTCGTCCA	35	40
-CRISPRs	10608	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTGAAATAACCCCCATAGCGGTGGCCATGGGGGCGTTTTACTAA	35	44
-CRISPRs	10687	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CATATCTGTTAGCTCAATTTGAGCAAGTTCATCATTTTTTA	35	41
diff -r db0f5c1cb227 -r 222b7f7b8432 test-data/crt.tabular
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/crt.tabular	Tue Jun 13 08:25:06 2017 -0400
@@ -0,0 +1,142 @@
+CRISPRs	1	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GATTGTTGTGCCCCTGGCGGTCGCTTTCAATGCCT	37	35
+CRISPRs	73	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TAATCCTAATTAGGTTTGAGTTAGTATCTAGTGCCAT	37	37
+CRISPRs	147	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ACAGATTTTGCTTCAGCTAGTACCAAAGGCTAG	37	33
+CRISPRs	217	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCGTAACTACCTTCTAAGTCTGTAGCGATGAATGTGG	37	37
+CRISPRs	291	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CAAAATATAGGGAAGAATTTTAGAAAGAACCTCAGAA	37	37
+CRISPRs	365	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AACTAAGGCATCCCATAGCATTCCGCTACGATCTATCAG	37	39
+CRISPRs	441	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TAATAATTGCTGATTAATCGTGGTGGTGGTGGTGG	37	35
+CRISPRs	513	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GATATATGGCTAAATATTGCTCAAAAGATTTTAATA	37	36
+CRISPRs	586	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATTAGATTGGTCGTGTTTTGATTAACGGTGCTAGC	37	35
+CRISPRs	658	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTGCCATCCCAGGCAACATAGCAAGCATGGAGGTG	37	35
+CRISPRs	730	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTGCCATCCCAGGCAACATAGCAAGCATGGAGGTG	37	35
+CRISPRs	802	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTGCGGACAGACTCGATTAAGTCAATAACAGCTTGG	37	36
+CRISPRs	875	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CTTGCCCTAATTTTCCTGGTGGAAAAGCCGCTGGCT	37	36
+CRISPRs	948	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATAGCAAGTTGCTAGAGAAAGCGCAACAAAACAAG	37	35
+CRISPRs	1020	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GAGGTTAAATTGTTGTCGATTCAAGAAGACTTGA	37	34
+CRISPRs	1091	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AATAGACACGAATTCCGGTTCCAGACCCAGCCCGTT	37	36
+CRISPRs	1164	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTCTTCCATCAGTCCAAGTTCTTCAACAATGTCTA	37	35
+CRISPRs	1236	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TGCTGAAGAAGCTGGAGAGAATCGGGCATCGCTAT	37	35
+CRISPRs	1308	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATTCCAGATGTGGTGGAAGAAACCTACGCCCCCGA	37	35
+CRISPRs	1380	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AATCAGCTTCCGGCGTTGCCATTTGGATTCAA	37	32
+CRISPRs	1449	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GTGAGGGGGCCAGATCCCTGCCAGATCCCCCAAT	37	34
+CRISPRs	1520	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATTAGATCTTTGGCATAAGGCAACCGAAACTGATC	37	35
+CRISPRs	1592	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GATTATCGTGCTTCCTTCGATGCTAACTTTGCTCT	37	35
+CRISPRs	1664	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCCATAATGATTCTGCCTCGTTTCTACTTGGTTTA	37	35
+CRISPRs	1736	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TGTATGTCACGCCATCGGACAGGTAGGGAAAGCCTGG	37	37
+CRISPRs	1810	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CAACTGGCTAAGCTGGTCATAAGGCTTTGGGAATGAAA	37	38
+CRISPRs	1885	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCGGGTTTCCCTCCTGGGTAATGACGCCTACGGG	37	34
+CRISPRs	1956	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CAAAGCTGGCACGGAAGCCCTTAAGGATATCCTC	37	34
+CRISPRs	2027	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GATGCAGAGATTCCACCACCAAAGGAGAATCCGATAA	37	37
+CRISPRs	2101	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAG	37	37
+CRISPRs	2175	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGG	37	41
+CRISPRs	2253	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAG	37	37
+CRISPRs	2327	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGG	37	41
+CRISPRs	2405	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AAGTAAGGTTCAAACGCCGCTACGCAGTCTGGTCC	37	35
+CRISPRs	2477	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CAAAGTTGGAACGAAAGCTAACGACAAAAACTA	37	33
+CRISPRs	2547	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTTAGCCATCGTCGGATTCTAATCGATCCAAAAGTCGG	37	38
+CRISPRs	2622	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	AATCCTACCAAGCGGCTTTTGGTGGGCCTGGCTCCGA	37	37
+CRISPRs	2696	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTCGGTTGATTGATGAAGATCTGATCGTCGAGTGGT	37	36
+CRISPRs	2769	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCCCTTTTCGGGGATAGGTGGTGTCCCTTTTCGG	37	34
+CRISPRs	2840	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ACTACCAGGGGGAAATTGATGGTATTCCCGGCAAA	37	35
+CRISPRs	2912	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ACTACCAGGGGGAAATTGATGGTATTCCCGGCAAA	37	35
+CRISPRs	2984	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GGGCAATGTTAAGCATGGCTAGAAGGAATAGTTAAC	37	36
+CRISPRs	3057	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TTCCATTAATGATTCTTCAAAAATCACTCGATT	37	33
+CRISPRs	3127	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	ACTGTTACTAGCCACCGCCCAACTCCTTTAATACTT	37	36
+CRISPRs	3200	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCTTCTGTTACGTAGATTTTTCCTGTTTCGCCAACAG	37	37
+CRISPRs	3274	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	CATCGCTCCCAGCATATTGTCCTGAACGGTCGGCAAT	37	37
+CRISPRs	3348	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	GATTTTTCCAGTGATGGTGCATACCTAGCCGTAG	37	34
+CRISPRs	3419	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TAGTCCCTCCCACACTGCCAATATTTCTTCAT	37	32
+CRISPRs	3488	CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC	TCCGTCTGTATGACTTATACTCGCAAGGATT	37	31
+CRISPRs	3725	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGTAGTAGAACCAATCGGGGTCGTCAATAACTCCCG	37	36
+CRISPRs	3798	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGGGGCTTGGGGGGTTGGAGTCCCCGCCCCCGTGGTGGGA	37	40
+CRISPRs	3875	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGTGAGTTGCATAATGCCTCCTAATGGCTGTTGGACTCATAA	37	42
+CRISPRs	3954	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTTGGTATTTGTAGTTCTCGATGAGTGTTTTAGGCA	37	36
+CRISPRs	4027	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGATAACGGGATGCCAGCCCTAAAGGTGATGAGCGG	37	36
+CRISPRs	4100	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGTTATCCGGCAAAGAAACCACACTACTAAGCTCGACAA	37	39
+CRISPRs	4176	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGGGCCGGGCGCGAGTTGTCCTCCTGTCCGAGGCCCCAC	37	39
+CRISPRs	4252	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGTTATCCGGCAAAGAAACCACACTACTAAGCTCGACAA	37	39
+CRISPRs	4328	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGGGCCGGGCGCGAGTTGTCCTCCTGTCCGAGGCCCCAC	37	39
+CRISPRs	4404	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTATTAAGGCTATTTTCGCCACTTCTGTTTGAAAG	37	35
+CRISPRs	4476	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GTCACACCTCTTCACGAATCCTCACATCATGAATAAGCTGCACA	37	44
+CRISPRs	4557	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGCGGGTCGAGATGTCGCTGGACACGCTGGTGCCGGACA	37	39
+CRISPRs	4633	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTGGGCGGACTGGAGTTGCCACCTGCCGATGGCCTGCA	37	38
+CRISPRs	4708	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GAGCCAAAGTCAACTAGCACAGGCACGGCAAGCCATCCTGA	37	41
+CRISPRs	4786	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TCGTGCATCTGCGCATAGGAAGAGGTTAATTCCTCAAC	37	38
+CRISPRs	4861	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AACGGGCAGCCCGAGTGGTGGGCATCGAGGTGGTGCTC	37	38
+CRISPRs	4936	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CCCCGCCACATTTTCGGATTAGAGGATTTGAATCGGCCGT	37	40
+CRISPRs	5013	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AGTTTCTCAAACTTTTCGGCGATCGCCGTCCAGGTGAGTTGA	37	42
+CRISPRs	5092	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TAGCGAAAAGTTATAGTTACCTTTGACCGGAGCTACCAACTCA	37	43
+CRISPRs	5172	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CCCCGCTGCCACGAGGGCAGCTGTAGACGCACCCC	37	35
+CRISPRs	5244	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TTAAATATACCCATCCCTAATAAAGGATAGAGATCTTGCA	37	40
+CRISPRs	5321	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GCTCTATTCTAATAACCCAAGCTTTTTTCAATTCTAA	37	37
+CRISPRs	5395	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CCGCTTGGTAGGATTGACCACCAAAGCTAGAAACAGGCACA	37	41
+CRISPRs	5473	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AGGGCGGTTAATCACTAGCGGCGATCTAGATATTG	37	35
+CRISPRs	5545	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TAGACTTCTATTTCCCCTCTTGCCGAGGGATGATACTGCAATTGA	37	45
+CRISPRs	5627	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TGCGCTCTCTTATCAAACGCCGCAACGCCATCAAGGCT	37	38
+CRISPRs	5702	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	ACGAGCGGAATCTTCTATGGATCGGATCACATCCTTAAT	37	39
+CRISPRs	5778	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTGGTGTCGGGGTTGTAGTATTCGTCTCGGTACAACA	37	37
+CRISPRs	5852	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	ACTATAGGGAGCGTTACCCTAGCTAGACATTGCCTAATCT	37	40
+CRISPRs	5929	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AAGAAGCAGAATAATGCGATTGAGTGGACAAAAATAAGAA	37	40
+CRISPRs	6006	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GGTTACGTATCGGCGTAACCGCCACTCCTTAGAG	37	34
+CRISPRs	6077	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGCCTCCTGCGCCCTGGAGGGGTGATCCTACACCTCGCG	37	39
+CRISPRs	6153	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GATTCTGGTATACGTTTATCCCACCACTCCTTAGCT	37	36
+CRISPRs	6226	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTCGTAAGCTAGGCAACGGCCTTGCTCGATGCACA	37	35
+CRISPRs	6298	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GGTGCAGCTGCGCCTAAGGAGATGGCTGTACAAGCT	37	36
+CRISPRs	6371	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CACCTAGAGGGTACCTCCCGGTTAGACCGGGGCTCTTAT	37	39
+CRISPRs	6447	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AACATGGCCACAACAACCTTCCCGGAGCAAGGGATG	37	36
+CRISPRs	6520	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GGCGATATTTGGCGTGCCAGCCAAGTGAATTTTGGCGCTG	37	40
+CRISPRs	6597	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	AACATGGCCACAACAACCTTCCCGGAGCAAGGGATG	37	36
+CRISPRs	6670	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GGCGATATTTGGCGTGCCAGCCAAGTGAATTTTGGCGCTG	37	40
+CRISPRs	6747	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CTAGCCTTTGTGGCTAACCCTCCTGCGCTTTGACATATAG	37	40
+CRISPRs	6824	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TTTTACCTCTTGCTCCTGCACAAGCTCAGCCTTAA	37	35
+CRISPRs	6896	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TCCTCCTCGCCTCTGAGAAAGAGTATGAAACACTGT	37	36
+CRISPRs	6969	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	ATGAACAGATTGCCATCTTCTAGGCGGATAGCCTGGG	37	37
+CRISPRs	7043	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGCCCATTGTTTGTGCTTCCGGAAGAAGTCTTTCAACTTC	37	40
+CRISPRs	7120	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GTTATCACGAGTTATCTTGCGCAAATCTTGTAGTGCATCTTTT	37	43
+CRISPRs	7200	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TTTAGCGGAGGAGACCTCTTCTATTTCTCCTATAACC	37	37
+CRISPRs	7274	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GGGAGAACCCTAAAAAGTTCTCCTGTCTAATCGCCACCTGT	37	41
+CRISPRs	7352	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CGCTCCAGAGTGCGCCGCCGCCGAATTGCGGTCCA	37	35
+CRISPRs	7424	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GAGACTCTATCTTTGGAGTTTCTAAGACATTGGCGGTTTCTAGGG	37	45
+CRISPRs	7506	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	ATTGCTTGGCGTAGGTTGACTTACCCGAGCCTGGGAGACCA	37	41
+CRISPRs	7584	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	TCCAAGGGCTCTTCGTCTTCAAAGGCCTTAGTTACCTCTG	37	40
+CRISPRs	7661	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	ATAATAAAGCACCCTCAACGGACTATGCCATGAACAACAGGACCC	37	45
+CRISPRs	7743	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	GTTGCCAGTTTTGCCGTTTTTGCTGTTCTGAGAT	37	34
+CRISPRs	7814	GTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC	CCCATAATAATTAGGCTCGCTACCATAAGGGGAAACTTCTTCCAAG	37	46
+CRISPRs	7945	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTTTAGGTGGGCGTTGACCTTTAGATTAGGAATGGT	35	37
+CRISPRs	8017	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAGCGCCACAGCTGACAGAGTTCCTGAAGGAAGCTAA	35	37
+CRISPRs	8089	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTGAGTGATTTTTATCAATTGTCGAGCTTAGTAGT	35	36
+CRISPRs	8160	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CACAGGAGTGTTAGCGCACTGCCTGTCATTACTATTA	35	37
+CRISPRs	8232	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTTAGATTGCGGGGGCTAGTGACGCCATAGTTTAACGACA	35	40
+CRISPRs	8307	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAAAGATATTAGGCTATCCTTCGGGGTAGTCTTTCTT	35	37
+CRISPRs	8379	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAAGTGTTGTTGCCTAGTGTTATACCAGAATATCCC	35	36
+CRISPRs	8450	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTCATTAGTGCTATCTTCTTGTTGATGGATTAGAACA	35	38
+CRISPRs	8523	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTCTACTCTGGTGAAGACCAAGTGGATTTCGTGGTGAT	35	38
+CRISPRs	8596	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CGTTAGTGCTTGGTTGTGGTTATGCTGCAACTAAGCC	35	37
+CRISPRs	8668	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CATCGATATACTTTTTAGCATCAGCTAAATGATAAAAA	35	38
+CRISPRs	8741	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTTAGAAAGTTTTGGTTAGTTTCCATTCCTCTTTTT	35	36
+CRISPRs	8812	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTTTCTCCATTGTTAGTTAGTCATTTCCTTGACAATT	35	37
+CRISPRs	8884	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTGGGATTCATGAACATGTTGATGGTGAATTATACCT	35	37
+CRISPRs	8956	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTGATTAAATTAATATGCGTGATAGATTAACTCATTTTGGTT	35	42
+CRISPRs	9033	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTTTTTTGGCATAACTCAGTAAGTCTTTTTTGTTTA	35	36
+CRISPRs	9104	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAATACTAATCTTAAAGATCTTGGTTTAATTACATATCGT	35	40
+CRISPRs	9179	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAACAATTGCAAGGTTTATAAGTAAATGAACAACAACG	35	38
+CRISPRs	9252	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAAATCCAACAACTTCTCCACATTTACTCCACTAGTCTC	35	39
+CRISPRs	9326	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTCCTACTTGTGCAGCCTCTAGTCCGCTTTTTAGATTGCG	35	41
+CRISPRs	9402	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CGCTTCGCTTCTTTCGCTTTCTCAACATAAAACTCATGAT	35	40
+CRISPRs	9477	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTAAAGTATGGTAACTCTGGGTAATTTTTTAACAG	35	36
+CRISPRs	9548	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCTTATCTTTTTCTAGCGTAACAAAAGAATAATCAGGA	35	38
+CRISPRs	9621	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTTTCAACCAAAAGCTTATTGGCTTCTACGGACTCACGAGC	35	41
+CRISPRs	9697	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTCTGAACTACTTTTTTTTCAACGACTTCACCATGGGAAG	35	40
+CRISPRs	9772	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAGTTTTAGATGCACCAATTACATCTTCTTCCATAAAGGA	35	40
+CRISPRs	9847	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CATTCAAGACCTCCGGTGGTCAGAAGACTGTAGCAACAAAGCTTGAG	35	47
+CRISPRs	9929	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTAGATCAGGCATCCAAACTCTTGGGCGATGTCGCGTAAC	35	40
+CRISPRs	10004	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CCGATGTAGCTCATAGCGACCTCGATAATTAATTGAT	35	37
+CRISPRs	10076	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CACCAAGCTAGTCACTATCCGATCAACCGTCGTTGCAGGT	35	40
+CRISPRs	10151	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTATCAAGAGTTGTCTAGTCAGTTCCAAGAAAAACCCTGGGAG	35	43
+CRISPRs	10229	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTGACCTGATTCCTCGAGAATTGAGACTCCTAAAGAAATTGC	35	42
+CRISPRs	10306	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAGTTCCAGTCGTGCTCCAAGGGCTCTTCGTCTTCA	35	36
+CRISPRs	10377	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CAACTTTGGAAAATTGCCTTCATACCATTCTTTTGTTAAACCGTTGTT	35	48
+CRISPRs	10460	GTCTCCACTCGCAGGAGAAATTAATTGATTGGAAA	CAGCAACAAAACAGCCAGCAGCAATTAATAAATCAGTT	35	38
+CRISPRs	10533	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CACTCCGTGGCGTCGTACCGGTACGCCTGGGCTTCGTCCA	35	40
+CRISPRs	10608	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CTGAAATAACCCCCATAGCGGTGGCCATGGGGGCGTTTTACTAA	35	44
+CRISPRs	10687	GTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA	CATATCTGTTAGCTCAATTTGAGCAAGTTCATCATTTTTTA	35	41
diff -r db0f5c1cb227 -r 222b7f7b8432 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri May 02 06:15:38 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,25 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <set_environment version="1.0">
-        <environment_variable name="CRISPR_RECOGNITION_TOOL_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
-    </set_environment>
-    <package name="crisper_recognition_tool" version="1.2">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://www.room220.com/crt/CRT1.2-CLI.jar.zip</action>
-                <action type="move_directory_files">
-                    <source_directory>.</source_directory>
-                    <destination_directory>$INSTALL_DIR</destination_directory>
-                </action>
-                <action type="set_environment">
-                    <environment_variable name="CRISPR_RECOGNITION_TOOL_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-        </readme>
-    </package>
-</tool_dependency>
-
-
-