# HG changeset patch
# User pjbriggs
# Date 1417448407 18000
# Node ID 3358c3d3014325c21ff92dd03200db4a5d5062c3

Uploaded initial version.

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
@@ -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
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
@@ -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;@###############################################################################################################################################
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
@@ -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;?;?##############################################################################
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
@@ -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<
diff -r 000000000000 -r 3358c3d30143 test-data/trimmomatic_pe_r1_unpaired_out1.fastq
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
@@ -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:?
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
@@ -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
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
@@ -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<
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
@@ -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
++
+=,,<=>>>@@
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
@@ -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>
+
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
+##
+#
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
@@ -0,0 +1,233 @@
+<tool id="trimmomatic" name="Trimmomatic" version="0.32.1">
+  <description>flexible read trimming tool for Illumina NGS data</description>
+  <command interpreter="bash">trimmomatic.sh
+  -mx8G
+  -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar
+  #if $paired_end.is_paired_end
+    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 
+  #else
+    SE -threads 6 -phred33 $fastq_in $fastq_out
+  #end if
+  ## ILLUMINACLIP option
+  #if $illuminaclip.do_illuminaclip
+    ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_DIR/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold
+  #end if
+  ## Other operations
+  #for $op in $operations
+    ## SLIDINGWINDOW
+    #if str( $op.operation.name ) == "SLIDINGWINDOW"
+      SLIDINGWINDOW:$op.operation.window_size:$op.operation.required_quality
+    #end if
+    ## MINLEN:36
+    #if str( $op.operation.name ) == "MINLEN"
+      MINLEN:$op.operation.minlen
+    #end if
+    #if str( $op.operation.name ) == "LEADING"
+      LEADING:$op.operation.leading
+    #end if
+    #if str( $op.operation.name ) == "TRAILING"
+      TRAILING:$op.operation.trailing
+    #end if
+    #if str( $op.operation.name ) == "CROP"
+      CROP:$op.operation.crop
+    #end if
+    #if str( $op.operation.name ) == "HEADCROP"
+      HEADCROP:$op.operation.headcrop
+    #end if
+  #end for
+  </command>
+  <requirements>
+    <requirement type="package" version="0.32">trimmomatic</requirement>
+  </requirements>
+  <inputs>
+    <conditional name="paired_end">
+    <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" />
+    <when value="no">
+      <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" />
+    </when>
+    <when value="yes">
+      <param name="fastq_r1_in" type="data" format="fastqsanger"
+	     label="Input FASTQ file (R1/first of pair)" />
+      <param name="fastq_r2_in" type="data" format="fastqsanger"
+	     label="Input FASTQ file (R2/second of pair)" />
+    </when>
+    </conditional>
+    <conditional name="illuminaclip">
+    <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" />
+    <when value="yes">
+      <param name="adapter_fasta" type="select" label="Adapter sequences to use">
+	<option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>
+	<option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>
+	<option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>
+	<option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>
+	<option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>
+	<option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>
+      </param>
+      <param name="seed_mismatches" type="integer" label="Maximum mismatch count which will still allow a full match to be performed" value="2" />
+      <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" />
+      <param name="simple_clip_threshold" type="integer" label="How accurate the match between any adapter etc. sequence must be against a read" value="10" />
+    </when>
+    </conditional>
+    <repeat name="operations" title="Trimmomatic Operation" min="1">
+      <conditional name="operation">
+	<param name="name" type="select" label="Select Trimmomatic operation to perform">
+	  <option selected="true" value="SLIDINGWINDOW">Sliding window trimming (SLIDINGWINDOW)</option>
+	  <option value="MINLEN">Drop reads below a specified length (MINLEN)</option>
+	  <option value="LEADING">Cut bases off the start of a read, if below a threshold quality (LEADING)</option>
+	  <option value="TRAILING">Cut bases off the end of a read, if below a threshold quality (TRAILING)</option>
+	  <option value="CROP">Cut the read to a specified length (CROP)</option>
+	  <option value="HEADCROP">Cut the specified number of bases from the start of the read (HEADCROP)</option>
+	</param>
+	<when value="SLIDINGWINDOW">
+	  <param name="window_size" type="integer" label="Number of bases to average across" value="4" />
+	  <param name="required_quality" type="integer" label="Average quality required" value="20" />
+	</when>
+	<when value="MINLEN">
+	  <param name="minlen" type="integer" label="Minimum length of reads to be kept" value="20" />
+	</when>
+	<when value="LEADING">
+	  <param name="leading" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the start of the read with quality below the threshold will be removed" />
+	</when>
+	<when value="TRAILING">
+	  <param name="trailing" type="integer" label="Minimum quality required to keep a base" value="3" help="Bases at the end of the read with quality below the threshold will be removed" />
+	</when>
+	<when value="CROP">
+	  <param name="crop" type="integer" label="Number of bases to keep from the start of the read" value="" />
+	</when>
+	<when value="HEADCROP">
+	  <param name="headcrop" type="integer" label="Number of bases to remove from the start of the read" value="" />
+	</when>
+      </conditional>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data format="fastqsanger" name="fastq_out_r1_paired" label="${tool.name} on ${on_string} (R1 paired)">
+      <filter>paired_end['is_paired_end']</filter>
+    </data>
+    <data format="fastqsanger" name="fastq_out_r1_unpaired" label="${tool.name} on ${on_string} (R1 unpaired)">
+      <filter>paired_end['is_paired_end']</filter>
+    </data>
+    <data format="fastqsanger" name="fastq_out_r2_paired" label="${tool.name} on ${on_string} (R2 paired)">
+      <filter>paired_end['is_paired_end']</filter>
+    </data>
+    <data format="fastqsanger" name="fastq_out_r2_unpaired" label="${tool.name} on ${on_string} (R2 unpaired)">
+      <filter>paired_end['is_paired_end']</filter>
+    </data>
+    <data format="fastqsanger" name="fastq_out" label="${tool.name} on ${on_string}">
+      <filter>not paired_end['is_paired_end']</filter>
+    </data>
+  </outputs>
+  <tests>
+    <test>
+      <!-- Single-end example -->
+      <param name="is_paired_end" value="no" />
+      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
+      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
+      <!-- 
+      **NB** outputs have to be specified in order that they appear in the
+      tool (which is the order they will be written to the history) - the
+      test framework seems to use the order and ignores the "name" attribute
+      -->
+      <output name="fastq_out" file="trimmomatic_se_out1.fastq" />
+    </test>
+    <test>
+      <!-- Paired-end example -->
+      <param name="is_paired_end" value="yes" />
+      <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
+      <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />
+      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
+      <!-- 
+      **NB** outputs have to be specified in order that they appear in the
+      tool (which is the order they will be written to the history) - the
+      test framework seems to use the order and ignores the "name" attribute
+      -->
+      <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1.fastq" />
+      <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
+      <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />
+      <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
+    </test>
+    <test>
+      <!-- Single-end example (cropping) -->
+      <param name="is_paired_end" value="no" />
+      <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
+      <param name="operations_0|operation|name" value="CROP" />
+      <param name="operations_0|operation|crop" value="10" />
+      <!-- 
+      **NB** outputs have to be specified in order that they appear in the
+      tool (which is the order they will be written to the history) - the
+      test framework seems to use the order and ignores the "name" attribute
+      -->
+      <output name="fastq_out" file="trimmomatic_se_out2.fastq" />
+    </test>
+  </tests>
+  <help>
+.. class:: infomark
+
+**What it does**
+
+Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and
+single ended data.
+
+This tool allows the following trimming steps to be performed:
+
+ * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read
+ * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average
+   quality within the window falls below a threshold
+ * **MINLEN:** Drop the read if it is below a specified length
+ * **LEADING:** Cut bases off the start of a read, if below a threshold quality
+ * **TRAILING:** Cut bases off the end of a read, if below a threshold quality
+ * **CROP:** Cut the read to a specified length
+ * **HEADCROP:** Cut the specified number of bases from the start of the read
+
+If ILLUMINACLIP is requested then it is always performed first; subsequent options
+can be mixed and matched and will be performed in the order that they have been
+specified.
+
+.. class:: warningmark
+
+Note that trimming operation order is important.
+
+-------------
+
+.. class:: infomark
+
+**Outputs**
+
+For paired-end data a particular strength of Trimmomatic is that it retains the
+pairing of reads (from R1 and R2) in the filtered output files:
+
+ * Two FASTQ files (R1-paired and R2-paired) contain one read from each pair where
+   both have survived filtering.
+ * Additionally two FASTQ files (R1-unpaired and R2-unpaired) contain reads where
+   one of the pair failed the filtering steps.
+
+Retaining the same order and number of reads in the filtered output fastq files is
+essential for many downstream analysis tools.
+
+For single-end data the output is a single FASTQ file containing just the filtered
+reads.
+
+-------------
+
+.. class:: infomark
+
+**Credits**
+
+This Galaxy tool has been developed within the Bioinformatics Core Facility at the
+University of Manchester. It runs the Trimmomatic program which has been developed
+within Bjorn Usadel's group at RWTH Aachen university.
+
+Trimmomatic website (including documentation):
+
+ * 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)
+
+Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you
+use it.
+  </help>
+</tool>