| Next changeset 1:2bd7cdbb6228 (2014-12-09) |
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Commit message:
Uploaded initial version. |
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added:
README.markdown test-data/Illumina_SG_R1.fastq test-data/Illumina_SG_R2.fastq test-data/trimmomatic_pe_r1_paired_out1.fastq test-data/trimmomatic_pe_r1_unpaired_out1.fastq test-data/trimmomatic_pe_r2_paired_out1.fastq test-data/trimmomatic_pe_r2_unpaired_out1.fastq test-data/trimmomatic_se_out1.fastq test-data/trimmomatic_se_out2.fastq tool_dependencies.xml trimmomatic.sh trimmomatic.xml |
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| diff -r 000000000000 -r 3358c3d30143 README.markdown --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.markdown Mon Dec 01 10:40:07 2014 -0500 |
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| @@ -0,0 +1,57 @@ +Trimmomatic +=========== + +XML tool file and shell script wrapper for the Trimmomatic program, which provides +various functions for manipluating Illumina FASTQ files. + +Trimmomatic has been developed within Bjorn Usadel's group at RWTH Aachen university: + + * <http://www.usadellab.org/cms/index.php?page=trimmomatic> + +The reference for Trimmomatic is: + + * Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a + user-friendly, integrated software solution for RNA-Seq-based transcriptomics. + Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7) + +Trimmomatic 0.32 can be obtained from: + + * <http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip> + +The tool assumes that two environment variables have been set, in order to find the +appropriate files: + + * `TRIMMOMATIC_DIR` should point to the directory holding the + `trimmomatic-0.32.jar` file, and + + * `TRIMMOMATIC_ADAPTERS_DIR` should point to the directory holding the adapter + sequence files (used by the `ILLUMINACLIP` option). + +Both variables will be set automatically if installing the tool dependencies e.g. via +a toolshed; otherwise they will need to be set manually in the Galaxy environment. + +To add to Galaxy add the following to tool_conf.xml: + + <tool file="trimmomatic/trimmomatic.xml" /> + +(The tool no longer uses a `.loc` file to point to the location of the adapter +sequence files) + +### Changes ### + +0.32.1: Remove `trimmomatic_adapters.loc.sample` and hard-code adapter files into + the XML wrapper. + +0.32.0: Add tool_dependencies.xml to install Trimmomatic 0.32 automatically and + (set the environment). Update tool versioning to use Trimmomatic version + number (i.e. `0.32`) with tool iteration appended (i.e. `.1`). + +0.0.4: Specify '-threads 6' in <command> section. + +0.0.3 : Added MINLEN, LEADING, TRAILING, CROP and HEADCROP options of trimmomatic. + +0.0.2: Updated ILLUMINACLIP option to use standard adapter sequences (requires the + trimmomatic_adapters.loc file; sample version is supplied) plus cosmetic + updates to wording and help text for some options. + +0.0.1: Initial version |
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| diff -r 000000000000 -r 3358c3d30143 test-data/Illumina_SG_R1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Illumina_SG_R1.fastq Mon Dec 01 10:40:07 2014 -0500 |
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| @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGGTAGGCAAGAATCACTGGATCAGCATAACAGATGAGGGTAGAGACGCCGTATCGTTTCTGGGCTAGGTTATCTGGGCCGCCTTCTTGCGTCGGCGCACAGTCACAAAGGAAATGCC ++ +?????BBB@BBBB?BBFFFF#66EAFHHHCEFEDFGHHHHF@DFHACEEF@FDFHHHHEEEHHHF?FGEHFHDEFGHHCEHEFHHHHFFFCFDFFFFBEEEEEEEEEEEB?EEEEEEEEEEEBBEE?CE?:ACCC*??CAAEECE:?ECA:?A*?EEEE?EEEE?0AAC/?8)00**0:8'8;48*?8/8?AEEEE8:A*8*0:**0**:?C?480?EE?A############################# +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGGTAGATACACCAGGAGGGATGAGAGTTGAGCGAGTTAGCTGTGGCCAGAGAGATGGGTCTAATCGTAGTCTACAACTGGGAGTCACATGCCACTACCGACTAATCTGGTCGCCGAACGGGAG ++ +?????BBBDDDDADDDE@FF#66CFCFHHBEHHIIIHIIHHFHHGHHHHHHHHHHIHIHIFHHHHHHEGFHIHHIIIHHHHHHHHCFHHHHHHHFFFFFFEEEEFFEFEEBBEEEFFE@E8;EEFFFEF*:AEEEEEFFFEAAEA?A?ACAEF?CEEFED2<.?AAECEAEFEEE8??A8?CAAE1?EEE?AE*888AEEEEFEEFFA8A8?ACEAEEEAE?C:??ED2<E:C*:?*:8?ED<>8.)8?< +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGGTTACCACTATACTCCCGTTTCTATATTCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGGTTGCCGTCTTCTGCTTGAAAAAAAAAAACAAACAAGAGAAGACGACGTACTGCACCACCA ++ +?<,<?BBBBBBBBBBBFFFF#6ACECCEC78CE=CGHEH7CHCHFGHADGHHHCCCHHE<DFHFFFFDFFFFFFDFDFDDEEEEEEEEECAEEEE;?BEEEBEEBCE;C;48;)?AACCEEE?AA?:?E88AEE:CE?AAEEEE:?***0:*??AAEEEEEEA?.8;E################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGGAGAAAGCGTCTTTTCCCGACTTGAATGGTTTGTCCCGACAGTTCGTTGACTGGGGTTTCGTCAGCCTTGAGCGGGGTTCCATCCATCTTTATCGCGCCTTGGGAAAGTAGTCGGCGGGCTTCGGGGTTGGGTGAGGGCAATCCTTGTTCGGTCAAAA ++ +5====>/<@@@@@@>@CCCE#66>ACEEEEGGGGGGGFFFEFDFFFFF=CDEFFFFEDEFFFFFC=AEBF-AA@CE;ECD5<5<==C==DEEE)83CD==@+4@DEE*<D1<)1@;888*90;*1988@)2)'4;=EE################################################################################################################ +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGGGTCACAGGGTCAGACTGGGTGACCTTCATGAAGCGTCTGGTGACGTAGCTGTGATAGTCCAGCTTGGCAACCTCTGCTGGTTGCAGAGG ++ +??,<?BBBDDDDDDD<FFF@FC;FFFBEFHHHCDDHHGHHHDGHHHFHHEA?EEAEEHDEFHHHHHFECFHHHFHDHEEHHCFH7CEFHDEHHCFHHFHHF=FFFDFDFFFFEEEEDDEFEEE<BBCEBCE,==AE1::AAEECEE*?*AAEFF??>D?)8):A8?EC?8***0*00:8?*)0*1:?CACC:AA?;)?EEFAEECE88*)1A*10*1:*1?:AC::A)*::*8ACEEE?########### +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA ++ +?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEE<DG8CC*??>DG.8<AGGGGCEEG*C2<GCCECE*:?CE?CE9C:C:C:?C*1**010:*?E82'2<GCE######## +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC +GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATTGGAGCATTTCTTTTGCAGTCAACTGCCAGTACATTAACTCCACTCTGTAATAGTAAATCCTGTCTCTTATCCACATCTCCGAGCCCACGAGAATAAGGCGA ++ +55,,5?9BBBBB<<BBFFFFFFFHHFBEFHFHHHFDFCF0A9@>9D9DFG;FHHHHGHHFFFFHHHHECDCEFF>EFEEEE@CDFEFHHGHHHHEHDGHHFHDFHFHHHHFFHHH@FDD??DFFFFDBBEEBEEEEEEEEEEEEEEEEE,;?CEC;CEEEECB?CEEEEEEEECEEE?C?CE*0?***/:::?:*/?:A::**/:*:ACE?0:::A::***00::*/?C888??EEE############# +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGGCCAGCCAAACCTGT ++ +?????BBBDBDDDDDDFFFFFFHIHIHHHHHHIHIFGGHFHHHHIIFHIHH?EEGHHHHHH-EGEHHCEHHHHH@FDFFEFF5@EEEFFEFE;AECCE;AEEEEEA?8?AEDDEEDFFDE2>>EEFF<<<2>D?DEEE*:C?AA<>8AEFCEE:?C?EEE?CEFEE0?:E?ACEECD8>EE>)8>E:CEEEEEED.)?AE??A?:A?*??:C0?CCE?AAA:88.88?::C:C?*8)4A?A######### +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAGTGCCAGAGATAGTGACCACAGTGTTGGCCCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAGACTTTTAAAAAACCGATCTACACCTTGACAGGCTATTAAAGGAAACTGGCCTGGTATCACAG ++ +=5===<>+5<5<+5=@CC;8CEEEEE;-8ACFDE.7C87CF-A>E>E=FFE**>>5AEDAEED-5-5AADC=D+=DDE<++3+CCD9DCD+=@3:DEEEEDD<@D*9DE99;@;@EE@;@@EEE7@@8@:@@@;9EE'449?<<E;=E<<;8(6;?############################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCTGCCCCTCCCTCCCTCACCAGCTAGCCTCCTATGCCGCGGTAGGGGGCTCAAAGAGATTCAGACACAGCCACGTAATCATGTTACTTGCCCATTCCCCCCTCCCTCCTCCTCCTCTCCCCCCCTCTCTTCCCCTCTCCCCTCCCCTCCTCCCCTCCTGTCCCTTATACACATC ++ +=,,<=>>>@@@@@9@@CCEE@EE+++6C8-++CECE+>DCC>@@EFFFFEEEDEE55+ACEF;-C+>EE++CBA--5A++CDC+4<<+=DE=CDEE@+@9D:D+4;@############################################################################################################################################### |
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| diff -r 000000000000 -r 3358c3d30143 test-data/Illumina_SG_R2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Illumina_SG_R2.fastq Mon Dec 01 10:40:07 2014 -0500 |
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| @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAGCGGGTCTATAATATTCTTGGCGAGGCTTGCAAACCTGGCCTGCGAGTGGT ++ +??A??ABBDDDDDDDDFFEEEFHIIIIHHIIHIFHIIHHHFHHIIIIIHHHFHHIIIIIIFFFHHIIHGDEHHAAEHHHHFHHHHD=EBBEEEEEFFFFEEEECEFFEEFFF8*??AA?;>DEEEFFFF*?8AECFEFFFFFFEAEEECFFFCEEEFFFFFFEEFEACEEC?CAACEFEEEFE?0?EACAAAEEAACEEA*.48.'0*1::A?CAA?CC::4''4'00'8:?A8?E############## +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATGTGACTCCCCGTTGTAGACTACGATTAGACCCATCTCTCTGGCCACAGCTAACTCGCTCAACTCTCATCCCTCCTGGGGTATCTACCAGCGATACGCGTAGAACTCGTGCCTCATGC ++ +?????BBBDDDDDDDDGFFGGGHHHHIHHHHHHHIHHHHIHBCEEHFFHHHIIHFHHHIIIIIIIHIFBGFGFHHHHIHE@EEEHHFFHHFF?CFHHHHHGGGGGGGGGGGGGGGGGGGECGGG;EE:CEGGG?#################################################################################################################### +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNCTAGNNCGCCGCTAAGACTGCCGTCAAATTCCTGAGCGGTAGTGATGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGCGCCGGCACATTCAAAAAAAAAAAACAGGAAAATGACATAGGCGTGTGTGA ++ +??AAABBBDDDDDEDDGGCFGGHHIFFHHH################################################################66?=##466@@EEEGCGGC>CE<EGEEGEGCEGEGGGG88<?1?C?EGCE?EEC?CC?CCEGGCGGCGC8?CCAC<AA'2228>*0*1C:?################################################################# +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCCGCCTACTTTCCCAAGGCGCGATAAAGATTGATGGAACCCCGCCCAAGGCTGACGAAATCCCCGCCAACGAACTGTCGGGCCGACCCATTCAAGTGGGGAAAAAAACCTTTCCCCGGGTTGACAAACCGCCAAACAACCTCACCAA ++ +????9B???AD9?BDDEEDDDDHHHHHFHFHFFHHHHHHHHHEHH>CEGHHFGHHGHH=FHHHHC+CGEBCC<CF@,4CF@CFBFFFFDF?B4BD@@D)>CE6BB)).).:AAAEE?A?A################################################################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGAGCCTCTGCAACCAGCAGAGGTTGCCAAGCTGGACTATCACAGCTACGTCACCAGACGCTTCATGAAGGTCACCCAGTCTGACCCTGTGAACCAGGCCGGG ++ +A??A?BBBDDDDDDDDGGGGGGHEFHHGEHHHIHEHHHHHDHBEHGFFFEGGDEEDGGGGGEGGEECE?EGCEGEGGGCEEEGGCEEGG4D;;4AGGGGGG8>GGA?EGGGEEGEEGGGCGGEGEGGGGD8<AADECECEGG?CCC:8CC''8:C:?CCE*?)0CC0:*?:C:?CCC8?CCEC9*::CCCC?C*::.CEGGEC99C4')).00*:C:?*10:CC########################## +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATTGAGAATCCGCTAGCGGATAAGATTTTGCGGGGGGAGTTGGCGGAGGGCGATCGCTTGATGCTTGATTATGGAGGGGAGGGGGAGAAGATAGGTTTTACGAAAATAGAGGCGGAGGGGTCGGCGGCATAGAGGGTAATTTTTTGGGTTTTTTTCTGTGTCTTATACACAACTGAACGTGCCGACGAGCGG ++ +?????@?BDDDDDDDDFEEEFFHIIHEHHHHDHHHHHEHHHHHH8ADFFFDFFD1D;>1,;;;;3B,3B;;*:B;1;''0::0*1:A*:;>DD'4'8.::AA>D22>DA>''0..08?*:A*1?:*0?########################################################################################################################## +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGAACAAG ++ +?????BBBDDDDDDDDGCFGFGIIIIIHFHIIIIHIHFG=EHHIGIIIIFHIHDGHGHHHIHIH=CGHGGHFHHHFHFGHHFH/ACDFGG?FE?CDFFHHHHHIIHFHHI>CEDGFHHHHHHHHDFHHFHHHFFAFFGGGGGGEDEG>>DACC;?EGG>CEEA>AEACCEE?:C::CC:::C:CE<C<9C:?C?*?CEECCC*:C?C?E:?:C:C:CCCCE:?C1*0*11.8C)2?'48>G######### +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCGTCCTGGTTTGCGTCGGGGATGCGGTCACCCTCTAAAAGATTTATGGAGGTCGTCTCTTGTGTCTGGGCCGGGGGGAAGATGT ++ +?????BBBDDDDDDDDGGGGGGIIHIIFHHHIHHIFHGHGGHHIHIIDEFFHEF@DFHIIHIIIGHACDCFFHHHIHIIHIHGHHHBGFGEEHHHHFHFFHHDFDCEGGFGGFGGG@DBEEEEGC>CEEGGGGGGE0?CDGGGD>EE2CE8CEGEE<>>>):CEEGDA'428CE:?9CC4828>'4<)0:>'04)1?E*8:1CC??):CCEECC**8)0548?C*:?:*010*:CC############## +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCCGTGGGCGCCGCATCATTAAAAAAAAAAAAAAAAAACATAACTCTCAAACGCGAATAGAGCAAGAAACAGACAGCTAAAGTACAAACAAT ++ +55<?????DDDBBDDBFFFFFFCHHIIHHIIIIIIIHGHHIIIIHHGHIIHFHHIIIIHHHCDHIIIHFFHIIIIICFFHIHECGCGEHIH=FHHHHHHHHHHF;FFFFFDDFFFFFFFEFFFFEFEBDFAEEAEE@EEDD>DDD880:?#################################################################################################### +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGAAGGGGGAATGAGCAAGTAACATAATTACATAGCTGTGTCTGAATCTCTTTGAGCACCCTACCTCGGCATAGGAGGCTAGCTGGTGAGGGAGGGAGGGGCAGACTGACAGGCCGAGGATGGCCTTGTGGTTGGCAAACTCCGTGGGGCGAGTCTGGGCTGCTGCATGCGCATCTGAGACTGGCTCTTGTACACATC ++ +?????@9@B?B?BBBBEEEFB@@EEHEC?BF-CE@DDEH,5+5C,>@+CE+<?=E-CFECEHHDBD,?DFF,4DDDBF;=B;;BBD;D,B4=BEEEEECB,,BB;?C?CEEEE*;;C:AC?C;?CC:AEEE?E8ACE:0:A?AA8A4.??8?8248)8:ACEEE?E)4;?;?############################################################################## |
| b |
| diff -r 000000000000 -r 3358c3d30143 test-data/trimmomatic_pe_r1_paired_out1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_pe_r1_paired_out1.fastq Mon Dec 01 10:40:07 2014 -0500 |
| b |
| @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNT ++ +?????BBB@BBBB?BBFFFF#6 +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNA ++ +?????BBBDDDDADDDE@FF#6 +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGG ++ +?<,<?BBBBBBBBBBBFFFF#6ACECCEC78CE=CGHEH7CHCHFGHADGHHHCCCHHE<DFHFFFFDFFFFFFDFDFDDEEEEEEEEECAEEEE;?BEEEBEEBCE;C;48; +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNT ++ +5====>/<@@@@@@>@CCCE#6 +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGG ++ +??,<?BBBDDDDDDD<FFF@FC;FFFBEFHHHCDDHHGHHHDGHHHFHHEA?EEAEEHDEFHHHHHFECFHHHFHDHEEHHCFH7CEFHDEHHCFHHFHHF=FFFDFDFFFFEEEEDDEFEEE<BBCEBCE,==AE1::AAEECEE*?*AAEFF??>D?)8 +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTA ++ +?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEE<DG8CC*??>DG.8<AGGGGCEEG*C2<GCCECE*:?CE?CE9C:C:C:?C +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGG ++ +?????BBBDBDDDDDDFFFFFFHIHIHHHHHHIHIFGGHFHHHHIIFHIHH?EEGHHHHHH-EGEHHCEHHHHH@FDFFEFF5@EEEFFEFE;AECCE;AEEEEEA?8?AEDDEEDFFDE2>>EEFF<<<2>D?DEEE*:C?AA<>8AEFCEE:?C?EEE?CEFEE0?:E?ACEECD8>EE>)8>E:CEEEEEED.)?AE??A?:A?*??:C0?CCE?AAA:88.88?::C:C?*8 +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGG ++ +=5===<>+5< |
| b |
| diff -r 000000000000 -r 3358c3d30143 test-data/trimmomatic_pe_r2_paired_out1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_pe_r2_paired_out1.fastq Mon Dec 01 10:40:07 2014 -0500 |
| b |
| @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC +GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACGATACGGCGTCTCTACCCTCATCTGTTATGCTGATCCAGTGATTCTTGCCTACCTTCTTTACGGTGATGTAATGCCAGTCGTTGGCAAG ++ +??A??ABBDDDDDDDDFFEEEFHIIIIHHIIHIFHIIHHHFHHIIIIIHHHFHHIIIIIIFFFHHIIHGDEHHAAEHHHHFHHHHD=EBBEEEEEFFFFEEEECEFFEEFFF8*??AA?;>DEEEFFFF*?8AECFEFFFFFFEAEEECFFFCEEEFFFFFFEEFEACEEC?CAACEFEEEFE?0?EACAAAEEAACEEA +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 2:N:0:NAAGGCGATAGATCGC +GATGACATCAGCACAGGTTCCGCTTCCGCTGTCGCAACGACGTGGCTGCCATCGATTATATTCAATTCTGAGTGCTGCCGTAGGGCTAGATGTAAGACTCACGTTCGGCGACCAGATTAGTCGGTAGTGGCATG ++ +?????BBBDDDDDDDDGFFGGGHHHHIHHHHHHHIHHHHIHBCEEHFFHHHIIHFHHHIIIIIIIHIFBGFGFHHHHIHE@EEEHHFFHHFF?CFHHHHHGGGGGGGGGGGGGGGGGGGECGGG;EE:CEGGG? +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 2:N:0:NAAGGCGATAGATCGC +GAATATAGAAACGGGAGTATAGTGGTAACC ++ +??AAABBBDDDDDEDDGGCFGGHHIFFHHH +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 2:N:0:NAAGGCGATAGATCGC +GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTGACCGAACAAGGATTGACCTCATCCAACTCCGAAGCCCGCC ++ +????9B???AD9?BDDEEDDDDHHHHHFHFHFFHHHHHHHHHEHH>CEGHHFGHHGHH=FHHHHC+CGEBCC<CF@,4CF@CFBFFFFDF?B4BD@@D)>CE6BB +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC +TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGACGGA ++ +A??A?BBBDDDDDDDDGGGGGGHEFHHGEHHHIHEHHHHHDHBEHGFFFEGGDEEDGGGGGEGGEECE?EGCEGEGGGCEEEGGCEEGG4D;;4AGGGGGG8>GGA?EGGGEEGEEGGGCGGEGEGGGGD8<AADECECEGG?CCC:8CC +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC +GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAGATT ++ +?????@?BDDDDDDDDFEEEFFHIIHEHHHHDHHHHHEHHHHHH8ADFFFDFFD1D;>1,; +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC +GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCGTACGGTCGAACACCACCACGAGGGTATCGGCG ++ +?????BBBDDDDDDDDGGGGGGIIHIIFHHHIHHIFHGHGGHHIHIIDEFFHEF@DFHIIHIIIGHACDCFFHHHIHIIHIHGHHHBGFGEEHHHHFHFFHHDFDCEGGFGGFGGG@DBEEEEGC>CEEGGGGGGE0?CDGGGD>EE2CE8CEGEE<>>>):CEEGDA +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC +GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAG ++ +55<?????DDDBBDDBFFFFFFCHHIIHHIIIIIIIHGHHIIIIHHGHIIHFHHIIIIHHHCDHIIIHFFHIIIIICFFHIHECGCGEHIH=FHHHHHHHHHHF;FFFFFDDFFFFFFFEFFFFEFEBDFAEEAEE@EEDD>DDD880:? |
| b |
| diff -r 000000000000 -r 3358c3d30143 test-data/trimmomatic_pe_r2_unpaired_out1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_pe_r2_unpaired_out1.fastq Mon Dec 01 10:40:07 2014 -0500 |
| b |
| @@ -0,0 +1,8 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTACCTGTCTCTTATACACA ++ +?????BBBDDDDDDDDGCFGFGIIIIIHFHIIIIHIHFG=EHHIGIIIIFHIHDGHGHHHIHIH=CGHGGHFHHHFHFGHHFH/ACDFGG?FE?CDFFHHHHHIIHFHHI>CEDGFHHHHHHHHDFHHFHHHFFAFFGGGGGGEDEG>>DACC;?EGG>CEEA>AEACCEE?:C::CC:::C:CE<C<9C:?C?*?CEECCC*:C?C?E:?:C:C:CCCCE:?C +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAG ++ +?????@9@B?B?BBBBEEEFB@@EEHEC?BF-CE@DDEH,5 |
| b |
| diff -r 000000000000 -r 3358c3d30143 test-data/trimmomatic_se_out1.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_se_out1.fastq Mon Dec 01 10:40:07 2014 -0500 |
| b |
| @@ -0,0 +1,32 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGAAGATAAAGAGNT ++ +?????BBB@BBBB?BBFFFF#6 +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCATCCGCCATTATNA ++ +?????BBBDDDDADDDE@FF#6 +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCGAGG ++ +?<,<?BBBBBBBBBBBFFFF#6ACECCEC78CE=CGHEH7CHCHFGHADGHHHCCCHHE<DFHFFFFDFFFFFFDFDFDDEEEEEEEEECAEEEE;?BEEEBEEBCE;C;48; +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGGGCTCAGCGCTNT ++ +5====>/<@@@@@@>@CCCE#6 +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGGTGAGGTTTCAGTACCTCTGGCCCGGCCTGG ++ +??,<?BBBDDDDDDD<FFF@FC;FFFBEFHHHCDDHHGHHHDGHHHFHHEA?EEAEEHDEFHHHHHFECFHHHFHDHEEHHCFH7CEFHDEHHCFHHFHHF=FFFDFDFFFFEEEEDDEFEEE<BBCEBCE,==AE1::AAEECEE*?*AAEFF??>D?)8 +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGCCTGTCTCTTA ++ +?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEE<DG8CC*??>DG.8<AGGGGCEEG*C2<GCCECE*:?CE?CE9C:C:C:?C +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGCAGACACCGACGGCACTAGTGCCACGGTATCAGGTACCACCATAACGTATGATTCGGGCACGCTCAAGGGCCAGCGTGACGGAATCGATAGAATACACTACACGGTGACTGATGGGG ++ +?????BBBDBDDDDDDFFFFFFHIHIHHHHHHIHIFGGHFHHHHIIFHIHH?EEGHHHHHH-EGEHHCEHHHHH@FDFFEFF5@EEEFFEFE;AECCE;AEEEEEA?8?AEDDEEDFFDE2>>EEFF<<<2>D?DEEE*:C?AA<>8AEFCEE:?C?EEE?CEFEE0?:E?ACEECD8>EE>)8>E:CEEEEEED.)?AE??A?:A?*??:C0?CCE?AAA:88.88?::C:C?*8 +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGG ++ +=5===<>+5< |
| b |
| diff -r 000000000000 -r 3358c3d30143 test-data/trimmomatic_se_out2.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_se_out2.fastq Mon Dec 01 10:40:07 2014 -0500 |
| b |
| @@ -0,0 +1,40 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC +AGATAGCCGA ++ +?????BBB@B +@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC +ATATATTCAT ++ +?????BBBDD +@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC +CATCACTACC ++ +?<,<?BBBBB +@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC +GAGCAGTCGG ++ +5====>/<@@ +@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC +GGTATCCCCC ++ +??,<?BBBDD +@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC +AAAATAATCC ++ +?????BBBDD +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC +GTAGTATTCT ++ +55,,5?9BBB +@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC +CTTCCCCACG ++ +?????BBBDB +@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC +GTGCAGGGGG ++ +=5===<>+5< +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC +TCTCAGATGA ++ +=,,<=>>>@@ |
| b |
| diff -r 000000000000 -r 3358c3d30143 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Dec 01 10:40:07 2014 -0500 |
| b |
| @@ -0,0 +1,27 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="trimmomatic" version="0.32"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip</action> + <action type="move_file"> + <source>trimmomatic-0.32.jar</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_directory_files"> + <source_directory>adapters</source_directory> + <destination_directory>$INSTALL_DIR/adapters</destination_directory> + </action> + <action type="set_environment"> + <environment_variable name="TRIMMOMATIC_DIR" action="set_to">$INSTALL_DIR</environment_variable> + </action> + <action type="set_environment"> + <environment_variable name="TRIMMOMATIC_ADAPTERS_DIR" action="set_to">$INSTALL_DIR/adapters</environment_variable> + </action> + </actions> + </install> + <readme>Trimmomatic requires the Java Runtime Environment + </readme> + </package> +</tool_dependency> + |
| b |
| diff -r 000000000000 -r 3358c3d30143 trimmomatic.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trimmomatic.sh Mon Dec 01 10:40:07 2014 -0500 |
| [ |
| @@ -0,0 +1,18 @@ +#!/bin/sh +# +# Shell wrapper to run Trimmomatic jar file as a Galaxy tool +echo Arguments: +for i in $@ ; do + echo "*" $i +done +java $@ 2>&1 | tee trimmomatic.log +status=$? +echo "Exit status: $status" +# Check for successful completion +if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then + echo "Trimmomatic did not finish successfully" >&2 + exit 1 +fi +exit $status +## +# |
| b |
| diff -r 000000000000 -r 3358c3d30143 trimmomatic.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trimmomatic.xml Mon Dec 01 10:40:07 2014 -0500 |
| b |
| b'@@ -0,0 +1,233 @@\n+<tool id="trimmomatic" name="Trimmomatic" version="0.32.1">\n+ <description>flexible read trimming tool for Illumina NGS data</description>\n+ <command interpreter="bash">trimmomatic.sh\n+ -mx8G\n+ -jar \\$TRIMMOMATIC_DIR/trimmomatic-0.32.jar\n+ #if $paired_end.is_paired_end\n+ PE -threads 6 -phred33 $fastq_r1_in $paired_end.fastq_r2_in $fastq_out_r1_paired $fastq_out_r1_unpaired $fastq_out_r2_paired $fastq_out_r2_unpaired \n+ #else\n+ SE -threads 6 -phred33 $fastq_in $fastq_out\n+ #end if\n+ ## ILLUMINACLIP option\n+ #if $illuminaclip.do_illuminaclip\n+ ILLUMINACLIP:\\$TRIMMOMATIC_ADAPTERS_DIR/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold\n+ #end if\n+ ## Other operations\n+ #for $op in $operations\n+ ## SLIDINGWINDOW\n+ #if str( $op.operation.name ) == "SLIDINGWINDOW"\n+ SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality\n+ #end if\n+ ## MINLEN:36\n+ #if str( $op.operation.name ) == "MINLEN"\n+ MINLEN:$op.operation.minlen\n+ #end if\n+ #if str( $op.operation.name ) == "LEADING"\n+ LEADING:$op.operation.leading\n+ #end if\n+ #if str( $op.operation.name ) == "TRAILING"\n+ TRAILING:$op.operation.trailing\n+ #end if\n+ #if str( $op.operation.name ) == "CROP"\n+ CROP:$op.operation.crop\n+ #end if\n+ #if str( $op.operation.name ) == "HEADCROP"\n+ HEADCROP:$op.operation.headcrop\n+ #end if\n+ #end for\n+ </command>\n+ <requirements>\n+ <requirement type="package" version="0.32">trimmomatic</requirement>\n+ </requirements>\n+ <inputs>\n+ <conditional name="paired_end">\n+ <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" />\n+ <when value="no">\n+ <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" />\n+ </when>\n+ <when value="yes">\n+ <param name="fastq_r1_in" type="data" format="fastqsanger"\n+\t label="Input FASTQ file (R1/first of pair)" />\n+ <param name="fastq_r2_in" type="data" format="fastqsanger"\n+\t label="Input FASTQ file (R2/second of pair)" />\n+ </when>\n+ </conditional>\n+ <conditional name="illuminaclip">\n+ <param name="do_illuminaclip" type="boolean" label="Perform initial ILLUMINACLIP step?" help="Cut adapter and other illumina-specific sequences from the read" truevalue="yes" falsevalue="no" checked="off" />\n+ <when value="yes">\n+ <param name="adapter_fasta" type="select" label="Adapter sequences to use">\n+\t<option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>\n+\t<option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>\n+\t<option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>\n+\t<option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>\n+\t<option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>\n+\t<option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>\n+ </param>\n+ <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" />\n+ <param name="palindrome_clip_threshold" type="integer" label="How accurate the match between the two \'adapter ligated\' reads must be for PE palindrome read alignment" value="30" />\n+ <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" />\n+ </when>\n+ </conditional>\n+ <repeat name="operations" title="Trimmomatic Operation" min="1">\n+ <conditional name="operation">\n+\t<param name="name" type="select" label="Select Trimmomatic operation to perform">\n+\t <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option>\n+\t <option value="MINLEN">Drop reads below a specified length (MINLEN)</opt'..b'_SG_R1.fastq" ftype="fastqsanger" />\n+ <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />\n+ <param name="operations_0|operation|name" value="SLIDINGWINDOW" />\n+ <!-- \n+ **NB** outputs have to be specified in order that they appear in the\n+ tool (which is the order they will be written to the history) - the\n+ test framework seems to use the order and ignores the "name" attribute\n+ -->\n+ <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" />\n+ <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />\n+ <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />\n+ <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />\n+ </test>\n+ <test>\n+ <!-- Single-end example (cropping) -->\n+ <param name="is_paired_end" value="no" />\n+ <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />\n+ <param name="operations_0|operation|name" value="CROP" />\n+ <param name="operations_0|operation|crop" value="10" />\n+ <!-- \n+ **NB** outputs have to be specified in order that they appear in the\n+ tool (which is the order they will be written to the history) - the\n+ test framework seems to use the order and ignores the "name" attribute\n+ -->\n+ <output name="fastq_out" file="trimmomatic_se_out2.fastq" />\n+ </test>\n+ </tests>\n+ <help>\n+.. class:: infomark\n+\n+**What it does**\n+\n+Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and\n+single ended data.\n+\n+This tool allows the following trimming steps to be performed:\n+\n+ * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read\n+ * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average\n+ quality within the window falls below a threshold\n+ * **MINLEN:** Drop the read if it is below a specified length\n+ * **LEADING:** Cut bases off the start of a read, if below a threshold quality\n+ * **TRAILING:** Cut bases off the end of a read, if below a threshold quality\n+ * **CROP:** Cut the read to a specified length\n+ * **HEADCROP:** Cut the specified number of bases from the start of the read\n+\n+If ILLUMINACLIP is requested then it is always performed first; subsequent options\n+can be mixed and matched and will be performed in the order that they have been\n+specified.\n+\n+.. class:: warningmark\n+\n+Note that trimming operation order is important.\n+\n+-------------\n+\n+.. class:: infomark\n+\n+**Outputs**\n+\n+For paired-end data a particular strength of Trimmomatic is that it retains the\n+pairing of reads (from R1 and R2) in the filtered output files:\n+\n+ * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where\n+ both have survived filtering.\n+ * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where\n+ one of the pair failed the filtering steps.\n+\n+Retaining the same order and number of reads in the filtered output fastq files is\n+essential for many downstream analysis tools.\n+\n+For single-end data the output is a single FASTQ file containing just the filtered\n+reads.\n+\n+-------------\n+\n+.. class:: infomark\n+\n+**Credits**\n+\n+This Galaxy tool has been developed within the Bioinformatics Core Facility at the\n+University of Manchester. It runs the Trimmomatic program which has been developed\n+within Bjorn Usadel\'s group at RWTH Aachen university.\n+\n+Trimmomatic website (including documentation):\n+\n+ * http://www.usadellab.org/cms/index.php?page=trimmomatic \n+\n+The reference for Trimmomatic is:\n+\n+ * Lohse M, Bolger AM, Nagel A, Fernie AR, Lunn JE, Stitt M, Usadel B. RobiNA: a\n+ user-friendly, integrated software solution for RNA-Seq-based transcriptomics.\n+ Nucleic Acids Res. 2012 Jul;40(Web Server issue):W622-7)\n+\n+Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you\n+use it.\n+ </help>\n+</tool>\n' |