| Next changeset 1:222b7f7b8432 (2017-06-13) |
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Commit message:
Imported from capsule None |
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added:
crt.xml readme.rst reformat.py test-data/crt.bed test-data/crt.tab test-data/sequence.fasta tool_dependencies.xml |
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| diff -r 000000000000 -r db0f5c1cb227 crt.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/crt.xml Fri May 02 06:15:38 2014 -0400 |
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| @@ -0,0 +1,74 @@ +<tool id="crispr_recognition_tool" name="CRISPR Recognition Tool" version="1.2.0"> + <description>(CRT)</description> + <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> + temp_output=\$(mktemp); + java -cp \$CRISPR_RECOGNITION_TOOL_JAR_PATH/CRT1.2-CLI.jar crt + -minNR $minNR + -minRL $minRL + -maxRL $maxRL + -minSL $minSL + -maxSL $maxSL + #if str($searchWL) != 'none': + -searchWL $searchWL + #end if + $input + \$temp_output + ; + + python \$CRISPR_RECOGNITION_TOOL_SCRIPT_PATH/reformat.py \$temp_output $output_region $output + </command> + <inputs> + <param format="fasta" name="input" type="data" label="Input sequence as FASTA"/> + + <param name="minNR" type="integer" value="3" label="Minimum number of repeats a CRISPER must have"/> + <param name="minRL" type="integer" value="19" label="Minimum length of a CRISPER repeated region"/> + <param name="maxRL" type="integer" value="38" label="Maximum length of a CRISPER repeated region"/> + <param name="minSL" type="integer" value="19" label="Minimum length of CRISPER non repeated region" help="or spacer region"/> + <param name="maxSL" type="integer" value="48" label="Maximum length of CRISPER non repeated region" help="or spacer region"/> + <param name="searchWL" type="select" label="Length of search window to used to discover CRISPERs"> + <option value="none" selected="true">default</option> + <option value="6">6</option> + <option value="7">7</option> + <option value="8">8</option> + <option value="9">9</option> + </param> + </inputs> + <outputs> + <data format="tabular" name="output" label="${tool.name} on ${on_string}" /> + <data format="bed" name="output_region" label="${tool.name} on ${on_string} - BED file" /> + </outputs> + <tests> + <test> + <param name="input" value="sequence.fasta" ftype="fasta" /> + <param name="minNR" value="3" /> + <param name="minRL" value="29" /> + <param name="maxRL" value="38" /> + <param name="minSL" value="19" /> + <param name="maxSL" value="48" /> + <param name="searchWL" value="none" /> + <output name="output" file="crt.tabular" ftype="tabular" /> + <output name="output_region" file="crt.bed" ftype="bed" /> + </test> + </tests> + <help> +CRISPR Recognition Tool - a tool for automatic detection of clustered regularly interspaced palindromic repeats + +http://www.room220.com/crt/ + +**Citation** + +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> +</tool> + |
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| diff -r 000000000000 -r db0f5c1cb227 readme.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/readme.rst Fri May 02 06:15:38 2014 -0400 |
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| @@ -0,0 +1,48 @@ +Galaxy wrapper for CRISPR RECOGNITION TOOL +========================================== + +This wrapper is copyright 2012-2013 by Björn Grüning and Omer Alkhnbashi + +This is a wrapper for the command line tool of CRT. + +CRISPR Recognition Tool - a tool for automatic detection of clustered regularly interspaced palindromic repeats + +http://www.room220.com/crt/ + +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` + + +Installation +============ + +Galaxy should be able to automatically install the dependencies. + + +History +======= + +v0.1 - Initial public release + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. + |
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| diff -r 000000000000 -r db0f5c1cb227 reformat.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/reformat.py Fri May 02 06:15:38 2014 -0400 |
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| @@ -0,0 +1,24 @@ +#!/usr/bin/env python + +""" + Extract importent information from the standard output file and put it in some standard format, like BED and tabular. +""" + +import sys + +bed = open(sys.argv[2], 'w+') +tabular = open(sys.argv[3], 'w+') + +for line in open(sys.argv[1]): + # ORGANISM: gi|21226102|ref|NC_003901.1| Methanosarcina mazei Go1 chromosome, complete genome + if line.startswith('ORGANISM:'): + organism = line.lstrip('ORGANISM:').strip() + # CRISPR 1 Range: 679197 - 682529 + if line.startswith('CRISPR '): + start,end = line.split('Range:')[1].strip().split('-') + start = start.strip() + end = end.strip() + bed.write('%s\t%s\t%s\n' % (organism, start, end)) + if line.rstrip().endswith(']'): + cols = line.split() + tabular.write("%s\t%s\t%s\t%s\t%s\t%s\n" % (organism, cols[0], cols[1], cols[2], cols[4].rstrip(','), cols[5])) |
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| diff -r 000000000000 -r db0f5c1cb227 test-data/crt.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crt.bed Fri May 02 06:15:38 2014 -0400 |
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| @@ -0,0 +1,3 @@ +CRISPRs 1 3592 +CRISPRs 3725 7933 +CRISPRs 7945 10797 |
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| diff -r 000000000000 -r db0f5c1cb227 test-data/crt.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/crt.tab Fri May 02 06:15:38 2014 -0400 |
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| b'@@ -0,0 +1,142 @@\n+CRISPRs\t1\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tGATTGTTGTGCCCCTGGCGGTCGCTTTCAATGCCT\t37\t35\n+CRISPRs\t73\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTAATCCTAATTAGGTTTGAGTTAGTATCTAGTGCCAT\t37\t37\n+CRISPRs\t147\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tACAGATTTTGCTTCAGCTAGTACCAAAGGCTAG\t37\t33\n+CRISPRs\t217\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTCGTAACTACCTTCTAAGTCTGTAGCGATGAATGTGG\t37\t37\n+CRISPRs\t291\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tCAAAATATAGGGAAGAATTTTAGAAAGAACCTCAGAA\t37\t37\n+CRISPRs\t365\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tAACTAAGGCATCCCATAGCATTCCGCTACGATCTATCAG\t37\t39\n+CRISPRs\t441\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTAATAATTGCTGATTAATCGTGGTGGTGGTGGTGG\t37\t35\n+CRISPRs\t513\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tGATATATGGCTAAATATTGCTCAAAAGATTTTAATA\t37\t36\n+CRISPRs\t586\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tATTAGATTGGTCGTGTTTTGATTAACGGTGCTAGC\t37\t35\n+CRISPRs\t658\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTTGCCATCCCAGGCAACATAGCAAGCATGGAGGTG\t37\t35\n+CRISPRs\t730\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTTGCCATCCCAGGCAACATAGCAAGCATGGAGGTG\t37\t35\n+CRISPRs\t802\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTTGCGGACAGACTCGATTAAGTCAATAACAGCTTGG\t37\t36\n+CRISPRs\t875\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tCTTGCCCTAATTTTCCTGGTGGAAAAGCCGCTGGCT\t37\t36\n+CRISPRs\t948\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tATAGCAAGTTGCTAGAGAAAGCGCAACAAAACAAG\t37\t35\n+CRISPRs\t1020\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tGAGGTTAAATTGTTGTCGATTCAAGAAGACTTGA\t37\t34\n+CRISPRs\t1091\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tAATAGACACGAATTCCGGTTCCAGACCCAGCCCGTT\t37\t36\n+CRISPRs\t1164\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTTCTTCCATCAGTCCAAGTTCTTCAACAATGTCTA\t37\t35\n+CRISPRs\t1236\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTGCTGAAGAAGCTGGAGAGAATCGGGCATCGCTAT\t37\t35\n+CRISPRs\t1308\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tATTCCAGATGTGGTGGAAGAAACCTACGCCCCCGA\t37\t35\n+CRISPRs\t1380\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tAATCAGCTTCCGGCGTTGCCATTTGGATTCAA\t37\t32\n+CRISPRs\t1449\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tGTGAGGGGGCCAGATCCCTGCCAGATCCCCCAAT\t37\t34\n+CRISPRs\t1520\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tATTAGATCTTTGGCATAAGGCAACCGAAACTGATC\t37\t35\n+CRISPRs\t1592\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tGATTATCGTGCTTCCTTCGATGCTAACTTTGCTCT\t37\t35\n+CRISPRs\t1664\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTCCATAATGATTCTGCCTCGTTTCTACTTGGTTTA\t37\t35\n+CRISPRs\t1736\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTGTATGTCACGCCATCGGACAGGTAGGGAAAGCCTGG\t37\t37\n+CRISPRs\t1810\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tCAACTGGCTAAGCTGGTCATAAGGCTTTGGGAATGAAA\t37\t38\n+CRISPRs\t1885\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTCGGGTTTCCCTCCTGGGTAATGACGCCTACGGG\t37\t34\n+CRISPRs\t1956\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tCAAAGCTGGCACGGAAGCCCTTAAGGATATCCTC\t37\t34\n+CRISPRs\t2027\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tGATGCAGAGATTCCACCACCAAAGGAGAATCCGATAA\t37\t37\n+CRISPRs\t2101\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tAAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAG\t37\t37\n+CRISPRs\t2175\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGG\t37\t41\n+CRISPRs\t2253\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tAAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAG\t37\t37\n+CRISPRs\t2327\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGG\t37\t41\n+CRISPRs\t2405\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tAAGTAAGGTTCAAACGCCGCTACGCAGTCTGGTCC\t37\t35\n+CRISPRs\t2477\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tCAAAGTTGGAACGAAAGCTAACGACAAAAACTA\t37\t33\n+CRISPRs\t2547\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTTTAGCCATCGTCGGATTCTAATCGATCCAAAAGTCGG\t37\t38\n+CRISPRs\t2622\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tAATCCTACCAAGCGGCTTTTGGTGGGCCTGGCTCCGA\t37\t37\n+CRISPRs\t2696\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTTCGGTTGATTGATGAAGATCTGATCGTCGAGTGGT\t37\t36\n+CRISPRs\t2769\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tTCCCTTTTCGGGGATAGGTGGTGTCCCTTTTCGG\t37\t34\n+CRISPRs\t2840\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tACTACCAGGGGGAAATTGATGGTATTCCCGGCAAA\t37\t35\n+CRISPRs\t2912\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tACTACCAGGGGGAAATTGATGGTATTCCCGGCAAA\t37\t35\n+CRISPRs\t2984\tCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAAC\tGGGCAATGTTAAGCATGGCTAGAAGGAATAGTTAAC\t37\t36\n+CRISPRs\t3057\tCTTT'..b'GTCTTCAAAGGCCTTAGTTACCTCTG\t37\t40\n+CRISPRs\t7661\tGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC\tATAATAAAGCACCCTCAACGGACTATGCCATGAACAACAGGACCC\t37\t45\n+CRISPRs\t7743\tGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC\tGTTGCCAGTTTTGCCGTTTTTGCTGTTCTGAGAT\t37\t34\n+CRISPRs\t7814\tGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAAC\tCCCATAATAATTAGGCTCGCTACCATAAGGGGAAACTTCTTCCAAG\t37\t46\n+CRISPRs\t7945\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCCTTTAGGTGGGCGTTGACCTTTAGATTAGGAATGGT\t35\t37\n+CRISPRs\t8017\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCAGCGCCACAGCTGACAGAGTTCCTGAAGGAAGCTAA\t35\t37\n+CRISPRs\t8089\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCCTGAGTGATTTTTATCAATTGTCGAGCTTAGTAGT\t35\t36\n+CRISPRs\t8160\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCACAGGAGTGTTAGCGCACTGCCTGTCATTACTATTA\t35\t37\n+CRISPRs\t8232\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTTAGATTGCGGGGGCTAGTGACGCCATAGTTTAACGACA\t35\t40\n+CRISPRs\t8307\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCAAAGATATTAGGCTATCCTTCGGGGTAGTCTTTCTT\t35\t37\n+CRISPRs\t8379\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCAAGTGTTGTTGCCTAGTGTTATACCAGAATATCCC\t35\t36\n+CRISPRs\t8450\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCCTCATTAGTGCTATCTTCTTGTTGATGGATTAGAACA\t35\t38\n+CRISPRs\t8523\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTCTACTCTGGTGAAGACCAAGTGGATTTCGTGGTGAT\t35\t38\n+CRISPRs\t8596\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCGTTAGTGCTTGGTTGTGGTTATGCTGCAACTAAGCC\t35\t37\n+CRISPRs\t8668\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCATCGATATACTTTTTAGCATCAGCTAAATGATAAAAA\t35\t38\n+CRISPRs\t8741\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTTAGAAAGTTTTGGTTAGTTTCCATTCCTCTTTTT\t35\t36\n+CRISPRs\t8812\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTTTCTCCATTGTTAGTTAGTCATTTCCTTGACAATT\t35\t37\n+CRISPRs\t8884\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTGGGATTCATGAACATGTTGATGGTGAATTATACCT\t35\t37\n+CRISPRs\t8956\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTGATTAAATTAATATGCGTGATAGATTAACTCATTTTGGTT\t35\t42\n+CRISPRs\t9033\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTTTTTTGGCATAACTCAGTAAGTCTTTTTTGTTTA\t35\t36\n+CRISPRs\t9104\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCAATACTAATCTTAAAGATCTTGGTTTAATTACATATCGT\t35\t40\n+CRISPRs\t9179\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCAACAATTGCAAGGTTTATAAGTAAATGAACAACAACG\t35\t38\n+CRISPRs\t9252\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCAAATCCAACAACTTCTCCACATTTACTCCACTAGTCTC\t35\t39\n+CRISPRs\t9326\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCCTCCTACTTGTGCAGCCTCTAGTCCGCTTTTTAGATTGCG\t35\t41\n+CRISPRs\t9402\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCGCTTCGCTTCTTTCGCTTTCTCAACATAAAACTCATGAT\t35\t40\n+CRISPRs\t9477\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCCTAAAGTATGGTAACTCTGGGTAATTTTTTAACAG\t35\t36\n+CRISPRs\t9548\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCCTTATCTTTTTCTAGCGTAACAAAAGAATAATCAGGA\t35\t38\n+CRISPRs\t9621\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTTTCAACCAAAAGCTTATTGGCTTCTACGGACTCACGAGC\t35\t41\n+CRISPRs\t9697\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTCTGAACTACTTTTTTTTCAACGACTTCACCATGGGAAG\t35\t40\n+CRISPRs\t9772\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCAGTTTTAGATGCACCAATTACATCTTCTTCCATAAAGGA\t35\t40\n+CRISPRs\t9847\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCATTCAAGACCTCCGGTGGTCAGAAGACTGTAGCAACAAAGCTTGAG\t35\t47\n+CRISPRs\t9929\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTAGATCAGGCATCCAAACTCTTGGGCGATGTCGCGTAAC\t35\t40\n+CRISPRs\t10004\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCCGATGTAGCTCATAGCGACCTCGATAATTAATTGAT\t35\t37\n+CRISPRs\t10076\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCACCAAGCTAGTCACTATCCGATCAACCGTCGTTGCAGGT\t35\t40\n+CRISPRs\t10151\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTATCAAGAGTTGTCTAGTCAGTTCCAAGAAAAACCCTGGGAG\t35\t43\n+CRISPRs\t10229\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTGACCTGATTCCTCGAGAATTGAGACTCCTAAAGAAATTGC\t35\t42\n+CRISPRs\t10306\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCAGTTCCAGTCGTGCTCCAAGGGCTCTTCGTCTTCA\t35\t36\n+CRISPRs\t10377\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCAACTTTGGAAAATTGCCTTCATACCATTCTTTTGTTAAACCGTTGTT\t35\t48\n+CRISPRs\t10460\tGTCTCCACTCGCAGGAGAAATTAATTGATTGGAAA\tCAGCAACAAAACAGCCAGCAGCAATTAATAAATCAGTT\t35\t38\n+CRISPRs\t10533\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCACTCCGTGGCGTCGTACCGGTACGCCTGGGCTTCGTCCA\t35\t40\n+CRISPRs\t10608\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCTGAAATAACCCCCATAGCGGTGGCCATGGGGGCGTTTTACTAA\t35\t44\n+CRISPRs\t10687\tGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAA\tCATATCTGTTAGCTCAATTTGAGCAAGTTCATCATTTTTTA\t35\t41\n' 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| diff -r 000000000000 -r db0f5c1cb227 test-data/sequence.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sequence.fasta Fri May 02 06:15:38 2014 -0400 |
| b |
| b'@@ -0,0 +1,2 @@\n+>CRISPRs\r\n+CTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATTGTTGTGCCCCTGGCGGTCGCTTTCAATGCCTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTAATCCTAATTAGGTTTGAGTTAGTATCTAGTGCCATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACAGATTTTGCTTCAGCTAGTACCAAAGGCTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCGTAACTACCTTCTAAGTCTGTAGCGATGAATGTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAAAATATAGGGAAGAATTTTAGAAAGAACCTCAGAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAACTAAGGCATCCCATAGCATTCCGCTACGATCTATCAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTAATAATTGCTGATTAATCGTGGTGGTGGTGGTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATATATGGCTAAATATTGCTCAAAAGATTTTAATACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTAGATTGGTCGTGTTTTGATTAACGGTGCTAGCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTGCCATCCCAGGCAACATAGCAAGCATGGAGGTGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTGCCATCCCAGGCAACATAGCAAGCATGGAGGTGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTGCGGACAGACTCGATTAAGTCAATAACAGCTTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCTTGCCCTAATTTTCCTGGTGGAAAAGCCGCTGGCTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATAGCAAGTTGCTAGAGAAAGCGCAACAAAACAAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGAGGTTAAATTGTTGTCGATTCAAGAAGACTTGACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAATAGACACGAATTCCGGTTCCAGACCCAGCCCGTTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTCTTCCATCAGTCCAAGTTCTTCAACAATGTCTACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTGCTGAAGAAGCTGGAGAGAATCGGGCATCGCTATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTCCAGATGTGGTGGAAGAAACCTACGCCCCCGACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAATCAGCTTCCGGCGTTGCCATTTGGATTCAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGTGAGGGGGCCAGATCCCTGCCAGATCCCCCAATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTAGATCTTTGGCATAAGGCAACCGAAACTGATCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATTATCGTGCTTCCTTCGATGCTAACTTTGCTCTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCCATAATGATTCTGCCTCGTTTCTACTTGGTTTACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTGTATGTCACGCCATCGGACAGGTAGGGAAAGCCTGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAACTGGCTAAGCTGGTCATAAGGCTTTGGGAATGAAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCGGGTTTCCCTCCTGGGTAATGACGCCTACGGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAAAGCTGGCACGGAAGCCCTTAAGGATATCCTCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATGCAGAGATTCCACCACCAAAGGAGAATCCGATAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAAAGATTGGGACTTTTAACTGCAAAATACCAGGCTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACATTTGTTGGGCCATCCTGCCCTGTCCATTGAGGTTAAGCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAAGTAAGGTTCAAACGCCGCTACGCAGTCTGGTCCCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCAAAGTTGGAACGAAAGCTAACGACAAAAACTACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTTAGCCATCGTCGGATTCTAATCGATCCAAAAGTCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACAATCCTACCAAGCGGCTTTTGGTGGGCCTGGCTCCGACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTCGGTTGATTGATGAAGATCTGATCGTCGAGTGGTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCCCTTTTCGGGGATAGGTGGTGTCCCTTTTCGGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACTACCAGGGGGAAATTGATGGTATTCCCGGCAAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACTACCAGGGGGAAATTGATGGTATTCCCGGCAAACTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGGGCAATGTTAAGCATGGCTAGAAGGAATAGTTAACCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTTCCATTAATGATTCTTCAAAAATCACTCGATTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACACTGTTACTAGCCACCGCCCAACTCCTTTAATACTTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCTTCTGTTACGTAGATTTTTCCTGTTTCGCCAACAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACCATCGCTCCCAGCATATTGTCCTGAACGGTCGGCAATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACGATTTTTCCAGTGATGGTGCATACCTAGCCGTAGCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTAGTCCCTCCCACACTGCCAATATTTCTTCATCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACTCCGTCTGTATGACTTATACTCGCAAGGATTCTTTCCTTCTACTAATCCCGGCGATCGGGACTGAAACNNNNNNNNATAGCCAAAAATAAGGCTTTTATTGTTATGTTTTCAGTACGTAACAAATCGTTAAACGTCTACCTCTTGTTTGGCGGATTGGCACCTCGAAAACCGCATACAGACTGTTTTTCAGTGTGATAGGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGTAGTAGAACCAATCGGGGTCGTCAATAACTCCCGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGGGGCTTGGGGGGTTGGAGTCCCCGCCCCCGTGGTGGGAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTGTGAGTTGCATAATGCCTCCTAATGGCTGTTGGACTCATAAGTTCAACACCCTCTTTTC'..b'CCTCCTGCGCTTTGACATATAGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTTTTACCTCTTGCTCCTGCACAAGCTCAGCCTTAAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTCCTCCTCGCCTCTGAGAAAGAGTATGAAACACTGTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACATGAACAGATTGCCATCTTCTAGGCGGATAGCCTGGGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGCCCATTGTTTGTGCTTCCGGAAGAAGTCTTTCAACTTCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGTTATCACGAGTTATCTTGCGCAAATCTTGTAGTGCATCTTTTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTTTAGCGGAGGAGACCTCTTCTATTTCTCCTATAACCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGGGAGAACCCTAAAAAGTTCTCCTGTCTAATCGCCACCTGTGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCGCTCCAGAGTGCGCCGCCGCCGAATTGCGGTCCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGAGACTCTATCTTTGGAGTTTCTAAGACATTGGCGGTTTCTAGGGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACATTGCTTGGCGTAGGTTGACTTACCCGAGCCTGGGAGACCAGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACTCCAAGGGCTCTTCGTCTTCAAAGGCCTTAGTTACCTCTGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACATAATAAAGCACCCTCAACGGACTATGCCATGAACAACAGGACCCGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACGTTGCCAGTTTTGCCGTTTTTGCTGTTCTGAGATGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACCCCATAATAATTAGGCTCGCTACCATAAGGGGAAACTTCTTCCAAGGTTCAACACCCTCTTTTCCCCGTCAGGGGACTGAAACNNNNNNNNNNNGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTTTAGGTGGGCGTTGACCTTTAGATTAGGAATGGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAGCGCCACAGCTGACAGAGTTCCTGAAGGAAGCTAAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTGAGTGATTTTTATCAATTGTCGAGCTTAGTAGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACACAGGAGTGTTAGCGCACTGCCTGTCATTACTATTAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTAGATTGCGGGGGCTAGTGACGCCATAGTTTAACGACAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAAAGATATTAGGCTATCCTTCGGGGTAGTCTTTCTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAAGTGTTGTTGCCTAGTGTTATACCAGAATATCCCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTCATTAGTGCTATCTTCTTGTTGATGGATTAGAACAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTCTACTCTGGTGAAGACCAAGTGGATTTCGTGGTGATGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACGTTAGTGCTTGGTTGTGGTTATGCTGCAACTAAGCCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACATCGATATACTTTTTAGCATCAGCTAAATGATAAAAAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTAGAAAGTTTTGGTTAGTTTCCATTCCTCTTTTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTTCTCCATTGTTAGTTAGTCATTTCCTTGACAATTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGGGATTCATGAACATGTTGATGGTGAATTATACCTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGATTAAATTAATATGCGTGATAGATTAACTCATTTTGGTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTTTTTGGCATAACTCAGTAAGTCTTTTTTGTTTAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAATACTAATCTTAAAGATCTTGGTTTAATTACATATCGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAACAATTGCAAGGTTTATAAGTAAATGAACAACAACGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAAATCCAACAACTTCTCCACATTTACTCCACTAGTCTCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTCCTACTTGTGCAGCCTCTAGTCCGCTTTTTAGATTGCGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACGCTTCGCTTCTTTCGCTTTCTCAACATAAAACTCATGATGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTAAAGTATGGTAACTCTGGGTAATTTTTTAACAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCTTATCTTTTTCTAGCGTAACAAAAGAATAATCAGGAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTTTCAACCAAAAGCTTATTGGCTTCTACGGACTCACGAGCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTCTGAACTACTTTTTTTTCAACGACTTCACCATGGGAAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAGTTTTAGATGCACCAATTACATCTTCTTCCATAAAGGAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACATTCAAGACCTCCGGTGGTCAGAAGACTGTAGCAACAAAGCTTGAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTAGATCAGGCATCCAAACTCTTGGGCGATGTCGCGTAACGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACCGATGTAGCTCATAGCGACCTCGATAATTAATTGATGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACACCAAGCTAGTCACTATCCGATCAACCGTCGTTGCAGGTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTATCAAGAGTTGTCTAGTCAGTTCCAAGAAAAACCCTGGGAGGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGACCTGATTCCTCGAGAATTGAGACTCCTAAAGAAATTGCGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAGTTCCAGTCGTGCTCCAAGGGCTCTTCGTCTTCAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACAACTTTGGAAAATTGCCTTCATACCATTCTTTTGTTAAACCGTTGTTGTCTCCACTCGCAGGAGAAATTAATTGATTGGAAACAGCAACAAAACAGCCAGCAGCAATTAATAAATCAGTTGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACACTCCGTGGCGTCGTACCGGTACGCCTGGGCTTCGTCCAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACTGAAATAACCCCCATAGCGGTGGCCATGGGGGCGTTTTACTAAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAACATATCTGTTAGCTCAATTTGAGCAAGTTCATCATTTTTTAGTCTCCACTCGTAGGAGAAATTAATTGATTGGAAAC\r\n' |
| b |
| diff -r 000000000000 -r db0f5c1cb227 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri May 02 06:15:38 2014 -0400 |
| b |
| @@ -0,0 +1,25 @@ +<?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> + + + |