| Previous changeset 0:2ac846969812 (2014-06-27) Next changeset 2:b007d9642911 (2015-07-16) |
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Commit message:
planemo upload for repository https://github.com/lparsons/galaxy_tools/tree/master/tools/fastq_join commit 394834f8f34909961cfbf6252fefbdc63342d78d |
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modified:
README.txt fastq-join.xml |
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removed:
test-data/test.sam test-data/testout.txt |
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| diff -r 2ac846969812 -r 593a729e5706 README.txt --- a/README.txt Fri Jun 27 15:39:38 2014 -0400 +++ b/README.txt Mon Jul 13 11:45:19 2015 -0400 |
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| @@ -1,19 +1,18 @@ -== fastq-join Galaxy Wrapper == +== fastq-join Galaxy Wrapper == -This is a Galaxy wrapper for the fastq-join tool from ea-utils suite. +This is a Galaxy wrapper for the fastq-join tool from ea-utils suite. -** Installation ** +** Installation ** -Installation from a tool shed provides the necessary tool dependencies. +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. +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 ** +** Attribution ** -The ea-utils package and associated documentation can be found at: http://code.google.com/p/ea-utils/ +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 +The galaxy wrapper code was written by Lance Parsons (lparsons@princeton.edu), Lewis-Sigler Institute for Integrative Genomics, Princeton University. |
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| diff -r 2ac846969812 -r 593a729e5706 fastq-join.xml --- a/fastq-join.xml Fri Jun 27 15:39:38 2014 -0400 +++ b/fastq-join.xml Mon Jul 13 11:45:19 2015 -0400 |
| [ |
| @@ -1,10 +1,16 @@ -<tool id="fastq_join" name="fastq-join" version="1.1.2-484"> - <description> - Joins paired-end reads on the overlapping ends</description> +<tool id="fastq_join" name="fastq-join" version="0.1.1"> + <description> - Joins two paired-end reads on the overlapping ends</description> + <requirements> <requirement type="package" version="1.1.2-484">ea-utils</requirement> </requirements> - <command> - fastq-join + + <stdio> + <exit_code range="1:" level="fatal" description="Unknown error occurred" /> + </stdio> + + <command><![CDATA[ + fastq-join -v '$splitChar' -p $pctMaxDiff -m $minOverlap @@ -13,8 +19,10 @@ #end if $read1 $read2 - -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined + -o $outputUnmatched1 -o $outputUnmatched2 -o $outputJoined + ]]> </command> + <inputs> <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read1" type="data" label="Read 1 Fastq" /> <param format="fastq, fastqillumina, fastqsanger, fastqsolexa" name="read2" type="data" label="Read 2 Fastq" /> @@ -25,18 +33,14 @@ </inputs> <outputs> - <data format="input" format_source="read1" name="outputJoined" label="${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 ${on_string} (unmatched2)"/> + <data format_source="read1" name="outputJoined" label="${tool.name} on ${on_string} (joined)"/> + <data format_source="read1" name="outputUnmatched1" label="${tool.name} on ${on_string} (unmatched1)"/> + <data format_source="read2" name="outputUnmatched2" label="${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" /> @@ -47,7 +51,7 @@ </test> </tests> - <help> + <help><![CDATA[ Overview -------- fastq-join joins two paired-end reads on the overlapping ends. @@ -61,5 +65,27 @@ 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> + + <citations> + <citation type="bibtex"> + @article{aronesty_comparison_2013, + title = {Comparison of {Sequencing} {Utility} {Programs}}, + volume = {7}, + issn = {18750362}, + url = {http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1}, + doi = {10.2174/1875036201307010001}, + language = {en}, + number = {1}, + urldate = {2015-07-10}, + journal = {The Open Bioinformatics Journal}, + author = {Aronesty, Erik}, + month = jan, + year = {2013}, + pages = {1--8} + } + </citation> + </citations> + </tool> |
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| diff -r 2ac846969812 -r 593a729e5706 test-data/test.sam --- a/test-data/test.sam Fri Jun 27 15:39:38 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,100 +0,0 @@\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 2ac846969812 -r 593a729e5706 test-data/testout.txt --- a/test-data/testout.txt Fri Jun 27 15:39:38 2014 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,29 +0,0 @@ -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 |