| Next changeset 1:593a729e5706 (2015-07-13) |
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Commit message:
Uploaded initial version with package dependency |
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added:
README.txt fastq-join.xml test-data/test.sam test-data/test_read1.fastq test-data/test_read3.fastq test-data/testout.join.fastq test-data/testout.txt test-data/testout.un1.fastq test-data/testout.un2.fastq tool_dependencies.xml |
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| diff -r 000000000000 -r 2ac846969812 README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.txt Fri Jun 27 15:39:38 2014 -0400 |
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| @@ -0,0 +1,19 @@ +== fastq-join Galaxy Wrapper == + +This is a Galaxy wrapper for the fastq-join tool from ea-utils suite. + +** Installation ** + +Installation from a tool shed provides the necessary tool dependencies. + +Otherwise, make sure fastq-join is in the path. +Move the test data files to your galaxy root test-data. +Move the xml files to a subdirectory of your tools directory and add lines in tool_conf.xml to point to them. +Restart the Galaxy server. + +** Attribution ** + +The ea-utils package and associated documentation can be found at: http://code.google.com/p/ea-utils/ + +The galaxy wrapper code was written by Lance Parsons (lparsons@princeton.edu), Lewis-Sigler Institute for Integrative Genomics, Princeton University. +The code is housed on BitBucket at: https://bitbucket.org/lance_parsons/ea_utils_galaxy_wrapper |
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| diff -r 000000000000 -r 2ac846969812 fastq-join.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/fastq-join.xml Fri Jun 27 15:39:38 2014 -0400 |
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| @@ -0,0 +1,65 @@ +<tool id="fastq_join" name="fastq-join" version="1.1.2-484"> + <description> - Joins paired-end reads on the overlapping ends</description> + <requirements> + <requirement type="package" version="1.1.2-484">ea-utils</requirement> + </requirements> + <command> + fastq-join + -v '$splitChar' + -p $pctMaxDiff + -m $minOverlap + #if $stitchLengthReport: + -r $outputStitchLengthReport + #end if + $read1 + $read2 + -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined + </command> + <inputs> + <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read1" type="data" label="Read 1 Fastq" /> + <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read2" type="data" label="Read 2 Fastq" /> + <param name="splitChar" type="text" value=" " label="Split read ids on this character" help="Default is space ' ' for Illumina reads" /> + <param name="pctMaxDiff" type="float" value="8" min="0" max="100" label="Maximum percentage difference between matching segments" /> + <param name="minOverlap" type="integer" value="6" min="1" label="Minimum length of matching segements" /> + <param name="stitchLengthReport" type="boolean" value="False" label="Output verbose stitch length report" /> + </inputs> + + <outputs> + <data format="input" format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/> + <data format="input" format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/> + <data format="input" format_source="read2" name="outputUnmatched2" label="${tool.name} on ${on_string} (unmatched2)"/> + <data format="tabular" name="outputStitchLengthReport" label="${tool.name} on ${on_string} (stitch length report)"> + <filter>stitchLengthReport</filter> + </data> + </outputs> + + <stdio> + <exit_code range="1:" level="fatal" description="Unknown error occurred" /> + </stdio> + + <tests> + <test> + <param name="read1" value="test_read1.fastq" /> + <param name="read2" value="test_read3.fastq" /> + <output name="outputJoined" file="testout.join.fastq" /> + <output name="outputUnmatched1" file="testout.un1.fastq" /> + <output name="outputUnmatched2" file="testout.un2.fastq" /> + </test> + </tests> + + <help> +Overview +-------- +fastq-join joins two paired-end reads on the overlapping ends. + +Split read ids character: Verifies that the 2 files probe id's match up to char C. Use ' ' for Illumina reads. + +Maximum difference is the maximum allowed percentage of bases that differ in the matching region. + +Minimum overlap is the minimum number of bases that must overlap (with no more than the maximum difference) for reads to be joined. + +Verbose stitch length report is a report for each joined paired of reads showing how large the overlapping section was. + +This tool uses sqr(distance)/len for anchored alignment quality algorithm. It's a good measure of anchored alignment quality, akin to squared-deviation for means. This tool uses the fastq-join program that is part of the ea-utils suite. See http://code.google.com/p/ea-utils/wiki/FastqJoin for details. + </help> +</tool> |
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| diff -r 000000000000 -r 2ac846969812 test-data/test.sam --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test.sam Fri Jun 27 15:39:38 2014 -0400 |
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| b'@@ -0,0 +1,100 @@\n+GEN-SEQ-ANA_0001:1:1:17434:14109#0/1\t0\tPCRPRIMER1\t5\t255\t33M\t*\t0\t0\tATACGGCGACCACCGAGATCTACACTCTTTCCC\t?<??>>BB>>A5AAA;;9:B<A?:AAA<B<AAA\tXA:i:0\tMD:Z:33\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:4183:5576#0/1\t0\tPCRPRIMER1+1\t1\t255\t38M\t*\t0\t0\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCCT\tAA=A=7=>;<BB8;>5>>?:B>BAABBBBBBBBABBB;\tXA:i:0\tMD:Z:38\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:16837:9043#0/1\t0\tPCRPRIMER1+1\t14\t255\t27M\t*\t0\t0\tCCACCGAGATCTACACTCTTTCCCTAC\t?BB?ABB?BBB<7A5?7??A?<AA?A?\tXA:i:0\tMD:Z:27\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:6753:19078#0/1\t0\tPCRPRIMER1+1\t58\t255\t25M\t*\t0\t0\tTAATGATACGGCGACCACCGAGATC\tA:BABA:AA<?B<<?BBBBBB@BBB\tXA:i:0\tMD:Z:25\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:14641:6640#0/1\t0\tPCRPRIMER1+1\t58\t255\t43M\t*\t0\t0\tTAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACAC\tAC@CB>:CC>CCCCCC?@CCBB<?@B@BAB@ABBBBBB5:?5?\tXA:i:0\tMD:Z:43\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:18498:19719#0/1\t0\tPCRPRIMER1+1\t58\t255\t38M\t*\t0\t0\tTAATGATACGGCGACCACCGAGATCTACACTCTTTCCC\tCCCCCCCCCBCCACCC@CCC@BCCCCCC@CCCCCCCCC\tXA:i:0\tMD:Z:38\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:5165:8271#0/1\t0\tPCRPRIMER1+2\t1\t255\t37M\t*\t0\t0\tAATGATACGGCGACCACCGAGATCTACACTCTTTCCC\tCC=CC>CC:@CCC@C>BAB<B>AAA88?>>ABBB:AA\tXA:i:0\tMD:Z:37\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:3890:20139#0/1\t0\tPCRPRIMER2+1\t34\t255\t23M\t*\t0\t0\tTAATGATACGGCGACCACCGAGA\tCCCCCC<CBB;;C@CC5<CABB7\tXA:i:0\tMD:Z:23\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:6236:11228#0/1\t0\tPCRPRIMER2+1\t34\t255\t20M\t*\t0\t0\tTAATGATACGGCGACCACCG\tCCCCCC8CCCCC=CC?AAAA\tXA:i:0\tMD:Z:20\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:13390:7511#0/1\t0\tPCRPRIMER2+1\t34\t255\t48M\t*\t0\t0\tTAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGC\tCCACBCBBBCCCCCCC?CCC;C?CCC?CCCCCCCCCCCACCCC;=>8A\tXA:i:0\tMD:Z:48\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:16810:9063#0/1\t0\tPCRPRIMER2+1\t34\t255\t45M\t*\t0\t0\tTAATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGA\tCCCCCCCCBCCCBBCCCCCCCCCCCCCCBA=@CCCCBC5B@9@@@\tXA:i:0\tMD:Z:45\tNM:i:0\n+GEN-SEQ-ANA_0001:1:1:1127:14386#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTGAATTCATGAATGGAAAAA\t?ACC<@>69@6>@BB?@:==\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1210:17845#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGAGATAATTCAAAATCTTGCCGAT\t>===>>@@@=<89A<B:@:BAA@@\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1260:17853#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTACAAATTCAGGACCACGCGTAAACGTCACC\tCCCCCB;ACBBB6@BB@BBB=A?A>6>AB?>B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1227:4069#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTCGAGAATTCTTTATCAACCTCGTT\t=CCCCCBC6@BCCC=9BA7A>>BB>\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1309:16895#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTACAAATTCCCTCATTCTTGGATTTGTA\tCA>CC@BBC8C@C>=C5<CCC@?CC;?>;\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1290:1939#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTACGTAATTCCGTGTCGGAGCCCGT\t??B:6>B;>AB=>B>B:BB>?A<6?\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1311:12611#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAAATTCGTTTATTTTTGTATTT\tBBBBB@@@@@@@B:====:BBA\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1312:13847#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tCGATAAATTCCTTGCTTCAACGATGCA\t?BB>=8CC@??CCCC@B?>CC:CCC:8\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1327:14127#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATAAATTCAGAATAGTTTCACT\t=A:??B>=;B@A;97C>B@=6B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1328:16612#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGAGATAATTCTTCTCATCGG\t@@@8@;C@C@CC=BC=>=AA\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1339:13574#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTTCTGTGATAATTTCAATATTGCC\tCB8B>=B=ABBBB:=BABBB@>=6\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1343:12008#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTTCGGCACTTTTCAGCACAATTTTCA\tCA=ACC@CC@BB=?AC??CC?CC?<C\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1353:17775#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tCGATAACTTCCCAACAGTGTTGTAAAG\t>5CBC?8?C=?ACBC>CCBB@=CAA8:\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1358:3384#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAACAAACCATGTTTTGCCCTCAAACAG\tB8:BBBBB:BBB=BBBA@<BBB>BB:9\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1361:15054#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tATGCTAATTCAGTAGCTATTGTTCTCCAAAT\tBCC:?CA?C?=CC?ABC@<?B@C@CC@8C>C\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1362:13972#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTAATTCTTCGCGAGTCTTTG\t@>C?CA?:@??@@@@CC?C?B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1363:2154#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tAGCTGAATTCTAGAAATGAAGAATATTTTTATTTATTTTCAG\tCB@C?B;CC=CAAC@@>:C?@:???CCBB>8>>>>?C>6>A?\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1373:2799#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGAGATAATTCAAAACTACTACTGTAGAGGGGTACTG\t?BABACCCC@B=<=@@?8B><@B@>BAAB9<@<>@B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1374:3530#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGAGATAATTCTTCCTCCTTAA\tAAAC8A=CA>CC@CC:B7ACC\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1379:7364#0/1'..b'CCC?\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1475:14575#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tTACGTAATTCGAAATTTGAG\t?CB@C==AA?C=CCCBB:@B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1480:6616#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTACAAATTCGAGCGCAAAGG\tC;CCCCCCC?C@C9CC?CCC:\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1481:5435#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTACAAATTATGAATAGAGAACTTTTA\tB@B6BBB=B>@@=@=@@BBBB>B?>B=\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1481:5276#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tGTACAAATTCGAATGAAATCATA\tCCCCBBCDB@C=CDACCC=C?C>\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:1482:10064#0/1\t4\t*\t0\t0\t*\t*\t0\t0\tCGATAAATTCAATTTGAAAA\tCC=CCC6C@;CCCBCAB?9B\tXM:i:0\n+GEN-SEQ-ANA_0001:1:1:148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| diff -r 000000000000 -r 2ac846969812 test-data/test_read1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_read1.fastq Fri Jun 27 15:39:38 2014 -0400 |
| b |
| @@ -0,0 +1,40 @@ +@JLK5VL1:222:D1888ACXX:1:1101:1656:2143 1:N:0: +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT ++ +?+:BDDDAD8BDD?@4+<?EECD?BBFIDFD<E:*?DI@?DDEDDCEECEIECDCCAD>5;6?;;@A;AABA>A@>AAAD;A>A>5=5>>>BBAA###### +@JLK5VL1:222:D1888ACXX:1:1101:1613:2167 1:N:0: +GTGATAGAGATACTGAGCACAGAGCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT ++ +@?BDFFFFHBHHHJJJGFEHHEIHEGHJJJJDI@DHIIHGGGGGEHIHGIIIIJJJGIB?AACBEDDFCDCCCCCEDC>@CD>CC@BA>CDEECD=BDDB> +@JLK5VL1:222:D1888ACXX:1:1101:1927:2121 1:N:0: +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT ++ +@B@DFFFFHHHHHJJIHJIJJJJJJJJJJJJIJHJJIJIJIHHGIJIIJGIIJJJIIII?EEEDFFFFEEEEEDECDDDEDDDDCCBACDEDECC@BB9<A +@JLK5VL1:222:D1888ACXX:1:1101:2000:2166 1:N:0: +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACGTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT ++ +B?@DFFFFHHHHHGIIJIIJJJJJJIJJJJJIIHIJJIJJIIGGJJGHGHIGGIIJHIGAEEEDFFEEEEFEEDDDDDCC>CCCCCACDDEEDCA9>BBDC +@JLK5VL1:222:D1888ACXX:1:1101:1763:2172 1:N:0: +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAAGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT ++ +@?@DDDBDHDFDHBFB3CCGFFHDHHIIIIIIG@<EFHA?DDFFDHHHHCHIIIIGGGH-;@5=CHHEADDEBEECCCCDCA@CCCB@CC@BC(;';BBBC +@JLK5VL1:222:D1888ACXX:1:1101:1832:2198 1:N:0: +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGCATATACCGCCAAT ++ +B=BDFFFFHGHHHJJIIJHIJIIJJJJJJJJIJIJJJIIJJHIIIJJJJIIIIJJIGJJ??CBBFFFFEDEEEEECDDCDDDCDCC@BDCDDEEC><>BD? +@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 1:N:0: +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTCGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT ++ +@?BFFFFFHHHHHJJJGIGIJIIJJJIGJJJJJJIIIIHGHIIGIJGIIIJJIJIIJJJEHDBDCDEEEEDDDDD@CCCDAA@CA@A:@CADD>C9<@B9C +@JLK5VL1:222:D1888ACXX:1:1101:2236:2214 1:N:0: +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT ++ +@=@DFDFFHAHDHGFEE@FFHGGEDEGHGIJ@GFGHAGFIIGBDGHIIJIGJJJJJIIIACEBDEFDFDEEEEDEDDCCDCD;CDCB@CF@DD@C?B<@DC +@JLK5VL1:222:D1888ACXX:1:1101:2090:2240 1:N:0: +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT ++ +@:?DDDDDF<FHHIIEEGBHGGDGGIIIGHIIIGGGHGEHFIHGIIIII<HHHIEGGIIHE=?BDECD@CDDCCCCCAAC@ACACCBCCDCDDDC###### +@JLK5VL1:222:D1888ACXX:1:1101:2952:2161 1:N:0: +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT ++ +@@@DFFFFHFHHGIJIJJJJJIJJJJIIIJJIIJJIJIEHIHIEHHIGJEHIIJIJDCGCE?BFFFDFEDDEEECACCCDDD@C>ABCCDCFFCA:9BBBC |
| b |
| diff -r 000000000000 -r 2ac846969812 test-data/test_read3.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test_read3.fastq Fri Jun 27 15:39:38 2014 -0400 |
| b |
| @@ -0,0 +1,40 @@ +@JLK5VL1:222:D1888ACXX:1:1101:1656:2143 3:N:0: +TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA ++ +BB8=4ADDHHHHACG<FHIGGIIIIICAEEC;CDF0@DEG3?BBACCGGICFD@@;@7;AED<<=CC@>(;(;@C@C:<:>>@>>;B>B(44?>C@B9<<8 +@JLK5VL1:222:D1888ACXX:1:1101:1613:2167 3:N:0: +TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA ++ +@?=DDDFFDFHHHIGGHHIGGFEGIJJFAFEGGGH@AFFHGIIIGEFHBF>@FCGAE@DD=D'9@DCC@;C@C@CDDCD>CCD@>>:@@C@CDDACA<28? +@JLK5VL1:222:D1888ACXX:1:1101:1927:2121 3:N:0: +TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA ++ +CCCFFFFFHHHHHJIIJJJJJJIJJJJIJJJJJJJIJJJJJJJJJJJJJJIHIJJIJEEHHF>BBDEFEDDDDDDDCDDDDCDDDEEEEDDDDDDDBDBDD +@JLK5VL1:222:D1888ACXX:1:1101:2000:2166 3:N:0: +TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA ++ +B@@DDFFFGHHHDIFHIJIIIJJJJIJJJJJIJJIIJIJIGIIJGIJJJJDFGGGII:DHFF<BDECDEDD@CCCDDCDDDCEDDDDC@C@CCDCD?@8<< +@JLK5VL1:222:D1888ACXX:1:1101:1763:2172 3:N:0: +TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA ++ +@;?DFDFFFDHHDIGACFHGGGGJJEH3@GDGCGHIEIIG?FDHCEGHEI9@C@C@@@9@=<',5;5;;;AC>3>C>CCCC(5(;>CDECCAC>@AB08AB +@JLK5VL1:222:D1888ACXX:1:1101:1832:2198 3:N:0: +TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATGCTTGTGAACAATGTGTATTCACTAACAACGTCA ++ +C@@FFFFFHHHHHJJJJJIJIJJJJIIJJIJIIFIGIJGHIDGIIIGIJJIHGHIIJGIIHF<<@DDDDEEDDCCCDDDCCCDDDEDDEDDCCDDCBB?AB +@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 3:N:0: +TTTGCCCTATTTATAGGACCCTAGAAAGAAAAAACCTCAAATAAAATAAAAGTGATTGGCGGGATATACTTGTGAACAATGTGTATTTACTTACCACCACC ++ +##################################################################################################### +@JLK5VL1:222:D1888ACXX:1:1101:2236:2214 3:N:0: +TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA ++ +@@@DDFFFHHHHFEEGIEHIJJGGFGIGIHCHJJJJJJIJIJGIGGIJIJGCDGEGG>EGHF=ABC@BDDCDDA@CCCCDCDE@CCD>CC@CDDDDBD?<< +@JLK5VL1:222:D1888ACXX:1:1101:2090:2240 3:N:0: +TGGATCCTATTAATAGGACCCTAGAAAGATAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA ++ +CC@FFFFFGFHDDHH>@FHHCHIIGIIEGGHIJIIBEEHIGGGGJIJJJJGBFGIGGCAHEA,9?B>B@@C>@@ACACCCC@C@@CDCDC@>CCCDD@(8? +@JLK5VL1:222:D1888ACXX:1:1101:2952:2161 3:N:0: +TGGATCCTATTAATAGGACCCTAGAAAGAAAAAACGCCAATCACAATAAAGTTGATTGGCGGTATATACTTGTGAACAATGTGTATTCACTAACAACGTCA ++ +CCCFFFFFHHHGHJJJJJIJJJJJIJJJHIJJIJJIIGIIIJEIIJIIJIG@FHIJJJIJHF<A?CBCC>CCDCCDDDDDDCDCCDDEACA@CDDDDDABB |
| b |
| diff -r 000000000000 -r 2ac846969812 test-data/testout.join.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testout.join.fastq Fri Jun 27 15:39:38 2014 -0400 |
| b |
| @@ -0,0 +1,36 @@ +@JLK5VL1:222:D1888ACXX:1:1101:1656:2143 +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA ++ +?+:BDDDAD8BDD?@4+<?EECD?BBFIDFD<E:*?DI@?DDEDDCEECEIECDCCADB@C>?;;@B>BABA@A@>AACDCA>A>5>@CC>BBDEA;7@;@@DFCIGGCCABB?3GED@0FDC;CEEACIIIIIGGIHF<GCAHHHHDDA4=8BB +@JLK5VL1:222:D1888ACXX:1:1101:1613:2167 +GTGATAGAGATACTGAGCACAGAGCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA ++ +@?BDFFFFHBHHHJJJGFEHHEIHEGHJJJJDI@DHIIHGGGGGEHIHGIIIIJJJGIBCADDCEDDFCDCCDCCEDCDDCDCCC@BCCDDEEDDDDDEBGCF@>FBHFEGIIIGHFFA@HGGGEFAFJJIGEFGGIHHGGIHHHFDFFDDD=?@ +@JLK5VL1:222:D1888ACXX:1:1101:1927:2121 +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA ++ +@B@DFFFFHHHHHJJIHJIJJJJJJJJJJJJIJHJJIJIJIHHGIJIIJGIIJJJIIIIDEEEDFFFFEEEEEDEDDDDEDDDDDDEFEDEDEFHHEEJIJJIHIJJJJJJJJJJJJJJIJJJJJJJIJJJJIJJJJJJIIJHHHHHFFFFFCCC +@JLK5VL1:222:D1888ACXX:1:1101:2000:2166 +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACGTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA ++ +B?@DFFFFHHHHHGIIJIIJJJJJJIJJJJJIIHIJJIJJIIGGJJGHGHIGGIIJHIGDEEEDFFEEEEFEEDDDDDDDCCCCDDEDDEEEDFFHDBIIGGGFDJJJJIGJIIGIJIJIIJJIJJJJJIJJJJIIIJIHFIDHHHGFFFDD@@B +@JLK5VL1:222:D1888ACXX:1:1101:1763:2172 +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAAGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA ++ +@?@DDDBDHDFDHBFB3CCGFFHDHHIIIIIIG@<EFHA?DDFFDHHHHCHIIIIGGGHA@@CACHHECDDEBEECCCCDCA@CCCB@CC@BC<=@;BBBC@C@9IEHGECHDF?GIIEIHGCGDG@3HEJJGGGGHFCAGIDHHDFFFDFD?;@ +@JLK5VL1:222:D1888ACXX:1:1101:1832:2198 +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGCATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA ++ +B=BDFFFFHGHHHJJIIJHIJIIJJJJJJJJIJIJJJIIJJHIIIJJJJIIIIJJIGJJCDDCCFFFFEEEEEEECDDDDDDDDEEDDDDDDEFHIIGJIIHGHIJJIGIIIGDIHGJIGIFIIJIJJIIJJJJIJIJJJJJHHHHHFFFFF@@C +@JLK5VL1:222:D1888ACXX:1:1101:2236:2214 +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA ++ +@=@DFDFFHAHDHGFEE@FFHGGEDEGHGIJ@GFGHAGFIIGBDGHIIJIGJJJJJIIIDDEDDEFDFDEEEEDEDDCCDCDDDDDDBCFBDDFHGE>GGEGDCGJIJIGGIGJIJIJJJJJJHCHIGIGFGGJJIHEIGEEFHHHHFFFDD@@@ +@JLK5VL1:222:D1888ACXX:1:1101:2090:2240 +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTATCTTTCTAGGGTCCTATTAATAGGATCCA ++ +@:?DDDDDF<FHHIIEEGBHGGDGGIIIGHIIIGGGHGEHFIHGIIIII<HHHIEGGIIHECCBDEDDDCDDCCCCCCACAACACCBCCDCDDDEHACGGIGFBGJJJJIJGGGGIHEEBIIJIHGGEIIGIIHCHHF@>HHDDHFGFFFFF@CC +@JLK5VL1:222:D1888ACXX:1:1101:2952:2161 +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTTGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAATCAACTTTATTGTGATTGGCGTTTTTTCTTTCTAGGGTCCTATTAATAGGATCCA ++ +@@@DFFFFHFHHGIJIJJJJJIJJJJIIIJJIIJJIJIEHIHIEHHIGJEHIIJIJDDGDEDCFFFDFEDDEEEDDDDDDDDDCCACCCDCFFFHJIJJJIHF@GIJIIJIIEJIIIGIIJJIJJIHJJJIJJJJJIJJJJJHGHHHFFFFFCCC |
| b |
| diff -r 000000000000 -r 2ac846969812 test-data/testout.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testout.txt Fri Jun 27 15:39:38 2014 -0400 |
| b |
| @@ -0,0 +1,29 @@ +reads 100 +version 1.32 +mapped reads 11 +mapped bases 377 +phred 33 +forward 0 +reverse 11 +len max 48 +len mean 34.2727 +len stdev 9.4137 +mapq mean 255.0000 +mapq stdev 0.0000 +mapq Q1 255.00 +mapq median 255.00 +mapq Q3 255.00 +snp rate 0.000000 +pct mismatch 0.0000 +base qual mean 31.5650 +base qual stdev 3.2627 +%A 27.5862 +%C 34.4828 +%G 16.7109 +%T 21.2202 +%PCRPRIMER1 8.753316 +%PCRPRIMER1+1 45.358090 +%PCRPRIMER1+2 9.814324 +%PCRPRIMER2+1 36.074271 +num ref seqs 4 +num ref aligned 4 |
| b |
| diff -r 000000000000 -r 2ac846969812 test-data/testout.un1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testout.un1.fastq Fri Jun 27 15:39:38 2014 -0400 |
| b |
| @@ -0,0 +1,4 @@ +@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 1:N:0: +GTGATAGAGATACTGAGCACAGACCCTTATTAAGCCGAGGGTCACCTAGCCAACTGACGTCGTTAGTGAATACACATTGTTCACAAGTATATACCGCCAAT ++ +@?BFFFFFHHHHHJJJGIGIJIIJJJIGJJJJJJIIIIHGHIIGIJGIIIJJIJIIJJJEHDBDCDEEEEDDDDD@CCCDAA@CA@A:@CADD>C9<@B9C |
| b |
| diff -r 000000000000 -r 2ac846969812 test-data/testout.un2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/testout.un2.fastq Fri Jun 27 15:39:38 2014 -0400 |
| b |
| @@ -0,0 +1,4 @@ +@JLK5VL1:222:D1888ACXX:1:1101:2169:2161 3:N:0: +TTTGCCCTATTTATAGGACCCTAGAAAGAAAAAACCTCAAATAAAATAAAAGTGATTGGCGGGATATACTTGTGAACAATGTGTATTTACTTACCACCACC ++ +##################################################################################################### |
| b |
| diff -r 000000000000 -r 2ac846969812 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Jun 27 15:39:38 2014 -0400 |
| b |
| @@ -0,0 +1,6 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ea-utils" version="1.1.2-484"> + <repository changeset_revision="ef9389074f0a" name="package_ea_utils_1_1_2_484" owner="lparsons" toolshed="https://toolshed.g2.bx.psu.edu" /> + </package> +</tool_dependency> |