# HG changeset patch
# User sanbi-uwc
# Date 1484917223 18000
# Node ID d8975856862e748ab9333c603c670e8953e02b39

planemo upload for repository https://github.com/SANBI-SA/galaxy-tools/tree/master/tools/trimmomatic commit 59bf1dad1e71026bff0431a020335c51ce1fd153

diff -r 000000000000 -r d8975856862e README.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/README.rst	Fri Jan 20 08:00:23 2017 -0500
@@ -0,0 +1,112 @@
+Trimmomatic: flexible read trimming tool for Illumina NGS data
+==============================================================
+
+Galaxy tool wrapper for the Trimmomatic program, which provides various functions for
+manipluating Illumina FASTQ files (both single and paired-end).
+
+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:
+
+- Bolger, A.M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer
+  for Illumina Sequence Data. Bioinformatics, btu170.
+
+Automated installation
+======================
+
+Installation via the Galaxy Tool Shed will take care of installing the tool wrapper
+and the trimmomatic program and data, and setting the appropriate environment
+variables.
+
+Manual Installation
+===================
+
+There are two files to install:
+
+- ``trimmomatic.xml`` (the Galaxy tool definition)
+- ``trimmomatic.sh`` (the shell script wrapper)
+
+The suggested location is in a ``tools/trimmomatic/`` folder. You will then
+need to modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool
+by adding the line:
+
+    <tool file="trimmomatic/trimmomatic.xml" />
+
+You will also need to install trimmomatic 0.36:
+
+- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip
+
+The tool wrapper uses the following environment variables in order to find the
+appropriate files:
+
+- ``TRIMMOMATIC_DIR`` should point to the directory holding the
+  ``trimmomatic-0.36.jar`` file
+- ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter
+  sequence files (used by the ``ILLUMINACLIP`` option).
+
+If you want to run the functional tests, copy the sample test files under
+sample test files under Galaxy's ``test-data/`` directory. Then:
+
+    ./run_tests.sh -id trimmomatic
+
+You will need to have set the environment variables above.
+
+History
+=======
+
+========== ======================================================================
+Version    Changes
+---------- ----------------------------------------------------------------------
+0.36.0     - Update to Trimmomatic 0.36.
+0.32.4     - Add support for ``AVGQUAL`` and ``MAXINFO`` operations.
+0.32.3     - Add support for FASTQ R1/R2 pairs using dataset collections (input
+             can be dataset collection, in which case tool also outputs dataset
+	     collections) and improve order and naming of output files.
+0.32.2     - Use ``GALAXY_SLOTS`` to set the appropriate number of threads to use
+             at runtime (default is 6).
+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
+========== ======================================================================
+
+
+Developers
+==========
+
+This tool is developed on the following GitHub repository:
+https://github.com/fls-bioinformatics-core/galaxy-tools/tree/master/trimmomatic
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball I use
+the ``package_trimmomatic.sh`` script.
+
+
+Licence (MIT)
+=============
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff -r 000000000000 -r d8975856862e install_tool_deps.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/install_tool_deps.sh	Fri Jan 20 08:00:23 2017 -0500
@@ -0,0 +1,22 @@
+#!/bin/bash
+#
+# Install dependencies for Trimmomatic for testing from the command line
+#
+# Installer functions
+. $(dirname $0)/../../local_dependency_installers/trimmomatic.sh
+# Installation directory
+TOP_DIR=$1
+if [ -z "$TOP_DIR" ] ; then
+    echo Usage: $(basename $0) DIR
+    exit
+fi
+if [ -z "$(echo $TOP_DIR | grep ^/)" ] ; then
+    TOP_DIR=$(pwd)/$TOP_DIR
+fi
+if [ ! -d "$TOP_DIR" ] ; then
+    mkdir -p $TOP_DIR
+fi
+# Trimmomatic 0.32
+install_trimmomatic_0_36 $TOP_DIR
+##
+#
diff -r 000000000000 -r d8975856862e package_trimmomatic.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/package_trimmomatic.sh	Fri Jan 20 08:00:23 2017 -0500
@@ -0,0 +1,24 @@
+#!/bin/sh
+#
+# Package Trimmomatic tool files into tgz file for upload to
+# Galaxy toolshed
+#
+TGZ=trimmomatic.tgz
+if [ -f $TGZ ] ; then
+    echo $TGZ: already exists, please remove >&2
+    exit 1
+fi
+tar cvzf $TGZ \
+    README.rst \
+    trimmomatic.xml \
+    trimmomatic.sh \
+    tool_dependencies.xml \
+    test-data
+if [ -f $TGZ ] ; then
+    echo Created $TGZ
+else
+    echo Failed to created $TGZ >&2
+    exit 1
+fi
+##
+#
diff -r 000000000000 -r d8975856862e run_planemo_tests.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/run_planemo_tests.sh	Fri Jan 20 08:00:23 2017 -0500
@@ -0,0 +1,39 @@
+#!/bin/bash
+#
+# Install dependencies and set up environment for
+# trimmomatic tool, then run tests using planemo
+#
+# Note that any arguments supplied to the script are
+# passed directly to the "planemo test..." invocation
+#
+# e.g. --install_galaxy (to get planemo to create a
+#                        Galaxy instance to run tests)
+#
+#      --galaxy_root DIR (to run tests using existing
+#                         Galaxy instance)
+#
+# List of dependencies
+TOOL_DEPENDENCIES="trimmomatic/0.36"
+# Where to find them
+TOOL_DEPENDENCIES_DIR=$(pwd)/test.tool_dependencies.trimmomatic
+if [ ! -d $TOOL_DEPENDENCIES_DIR ] ; then
+    echo WARNING $TOOL_DEPENDENCIES_DIR not found >&2
+    echo Creating tool dependencies dir
+    mkdir -p $TOOL_DEPENDENCIES_DIR
+    echo Installing tool dependencies
+    $(dirname $0)/install_tool_deps.sh $TOOL_DEPENDENCIES_DIR
+fi
+# Load dependencies
+for dep in $TOOL_DEPENDENCIES ; do
+    env_file=$TOOL_DEPENDENCIES_DIR/$dep/env.sh
+    if [ -e $env_file ] ; then
+	. $env_file
+    else
+	echo ERROR no env.sh file found for $dep >&2
+	exit 1
+    fi
+done
+# Run the planemo tests
+planemo test $@ $(dirname $0)/trimmomatic.xml
+##
+#
diff -r 000000000000 -r d8975856862e test-data/Illumina_SG_R1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Illumina_SG_R1.fastq	Fri Jan 20 08:00:23 2017 -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 d8975856862e test-data/Illumina_SG_R1.fastq.gz
Binary file test-data/Illumina_SG_R1.fastq.gz has changed
diff -r 000000000000 -r d8975856862e test-data/Illumina_SG_R2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/Illumina_SG_R2.fastq	Fri Jan 20 08:00:23 2017 -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 d8975856862e test-data/Illumina_SG_R2.fastq.gz
Binary file test-data/Illumina_SG_R2.fastq.gz has changed
diff -r 000000000000 -r d8975856862e test-data/trimmomatic_avgqual.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_avgqual.fastq	Fri Jan 20 08:00:23 2017 -0500
@@ -0,0 +1,16 @@
+@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:1:1101:15290:2442 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#########
diff -r 000000000000 -r d8975856862e test-data/trimmomatic_maxinfo.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_maxinfo.fastq	Fri Jan 20 08:00:23 2017 -0500
@@ -0,0 +1,40 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 1:N:0:NAAGGCGATAGATCGC
+AGATAGCCGAAGATAAAGAGNTCATAACCGTAAAGGCCAGAGACGAGAACCACTCGCAGGCAAGGTTTGCAAGCCTCGCCAAGAATATTATAGACCCGCTTGCCAACGACTGGCATTACATCACCGTAAAGAAGG
++
+?????BBB@BBBB?BBFFFF#66EAFHHHCEFEDFGHHHHF@DFHACEEF@FDFHHHHEEEHHHF?FGEHFHDEFGHHCEHEFHHHHFFFCFDFFFFBEEEEEEEEEEEB?EEEEEEEEEEEBBEE?CE?:ACCC
+@MISEQ:1:000000000-A2Y1L:1:1101:18667:2435 1:N:0:NAAGGCGATAGATCGC
+ATATATTCATCCGCCATTATNAGAGTCCGATTACTTTAGAACAGTGCCGCGAATCCTTCGTCAACTGTAATCCAAGCGACATTGGTTCGATTAGCACGCATGAGGCACGAGATCTACGCGTATCTCTGG
++
+?????BBBDDDDADDDE@FF#66CFCFHHBEHHIIIHIIHHFHHGHHHHHHHHHHIHIHIFHHHHHHEGFHIHHIIIHHHHHHHHCFHHHHHHHFFFFFFEEEEFFEFEEBBEEEFFE@E8;EEFFFEF
+@MISEQ:1:000000000-A2Y1L:1:1101:17523:2436 1:N:0:NAAGGCGATAGATCGC
+CATCACTACCGCTCAGGAATNTGACGGCAGTCTTAGCGGCGCTCTAGTGCGGGAGGCCGTATCTTGGAATAAGGTGTCGTCAAATGCAAGGCAGGTAACCCTACACGCCG
++
+?<,<?BBBBBBBBBBBFFFF#6ACECCEC78CE=CGHEH7CHCHFGHADGHHHCCCHHE<DFHFFFFDFFFFFFDFDFDDEEEEEEEEECAEEEE;?BEEEBEEBCE;C;
+@MISEQ:1:000000000-A2Y1L:1:1101:15489:2437 1:N:0:NAAGGCGATAGATCGC
+GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTGTGATTGGCGGTTAGTCAACTCGG
++
+5====>/<@@@@@@>@CCCE#66>ACEEEEGGGGGGGFFFEFDFFFFF=CDEFFFFEDEFFFFFC=AEBF-AA@CE;ECD5<5<==C==DEEE
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 1:N:0:NAAGGCGATAGATCGC
+GGTATCCCCCGGCAGTGAGGATGGAGCCATGGTCTGCATCATACTCACCGTAGGTGAGAATATCCACGTCCTTCGACTCCTGGGTGCCGTCTATGGTGCCCTCTGTTACCAGGCAGTGACGGAGGACATGG
++
+??,<?BBBDDDDDDD<FFF@FC;FFFBEFHHHCDDHHGHHHDGHHHFHHEA?EEAEEHDEFHHHHHFECFHHHFHDHEEHHCFH7CEFHDEHHCFHHFHHF=FFFDFDFFFFEEEEDDEFEEE<BBCEBCE
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 1:N:0:NAAGGCGATAGATCGC
+AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCC
++
+?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEE<DG
+@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 1:N:0:NAAGGCGATAGATCGC
+GTAGTATTCTCATATCACAAGTCCCCAAACTGCATAAGGTGTGGAGTGGAGTGTCTCCCACTGCATTTTGTTGGTTTGGGTTGCATTTTTTGTGGCACAAAATTATCTTTAAACACTCTAAGCTCATATTTGCACATGCAACATGAATT
++
+55,,5?9BBBBB<<BBFFFFFFFHHFBEFHFHHHFDFCF0A9@>9D9DFG;FHHHHGHHFFFFHHHHECDCEFF>EFEEEE@CDFEFHHGHHHHEHDGHHFHDFHFHHHHFFHHH@FDD??DFFFFDBBEEBEEEEEEEEEEEEEEEEE
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 1:N:0:NAAGGCGATAGATCGC
+CTTCCCCACGGCCCAGACACAAGAGACGACCTCCATAAATCTTTTAGAGGGTGACCGCATCTCCGACGCAAACCAGGACGCCGATACCCTCGTGGTGGTGTTCGACCGTACGGATGGCGC
++
+?????BBBDBDDDDDDFFFFFFHIHIHHHHHHIHIFGGHFHHHHIIFHIHH?EEGHHHHHH-EGEHHCEHHHHH@FDFFEFF5@EEEFFEFE;AECCE;AEEEEEA?8?AEDDEEDFFDE
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 1:N:0:TAAGGCGATAGATCGC
+GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCATGAGGTAGCAGACCAG
++
+=5===<>+5<5<+5=@CC;8CEEEEE;-8ACFDE.7C87CF-A>E>E=FFE**>>5AEDAEED-5-5AADC=D+=DDE<
+@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC
+TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAGGCCATCCTCGGCCTGTCAGCCT
++
+=,,<=>>>@@@@@9@@CCEE@EE+++6C8-++CECE+>DCC>@@EFFFFEEEDEE55+ACEF;-C+>EE++CBA--5A
diff -r 000000000000 -r d8975856862e 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	Fri Jan 20 08:00:23 2017 -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 d8975856862e test-data/trimmomatic_pe_r1_paired_out1.fastq.gz
Binary file test-data/trimmomatic_pe_r1_paired_out1.fastq.gz has changed
diff -r 000000000000 -r d8975856862e test-data/trimmomatic_pe_r1_unpaired_out1.fastq
diff -r 000000000000 -r d8975856862e test-data/trimmomatic_pe_r1_unpaired_out1.fastq.gz
Binary file test-data/trimmomatic_pe_r1_unpaired_out1.fastq.gz has changed
diff -r 000000000000 -r d8975856862e 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	Fri Jan 20 08:00:23 2017 -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 d8975856862e test-data/trimmomatic_pe_r2_paired_out1.fastq.gz
Binary file test-data/trimmomatic_pe_r2_paired_out1.fastq.gz has changed
diff -r 000000000000 -r d8975856862e 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	Fri Jan 20 08:00:23 2017 -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 d8975856862e test-data/trimmomatic_pe_r2_unpaired_out1.fastq.gz
Binary file test-data/trimmomatic_pe_r2_unpaired_out1.fastq.gz has changed
diff -r 000000000000 -r d8975856862e test-data/trimmomatic_se_out1.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_se_out1.fastq	Fri Jan 20 08:00:23 2017 -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 d8975856862e test-data/trimmomatic_se_out1.fastq.gz
Binary file test-data/trimmomatic_se_out1.fastq.gz has changed
diff -r 000000000000 -r d8975856862e test-data/trimmomatic_se_out2.fastq
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_se_out2.fastq	Fri Jan 20 08:00:23 2017 -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 d8975856862e tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Jan 20 08:00:23 2017 -0500
@@ -0,0 +1,27 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="trimmomatic" version="0.36">
+      <install version="1.0">
+	<actions>
+	  <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip</action>
+	  <action type="move_file">
+	    <source>trimmomatic-0.36.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 d8975856862e trimmomatic.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic.sh	Fri Jan 20 08:00:23 2017 -0500
@@ -0,0 +1,33 @@
+#!/bin/sh
+#
+# Shell wrapper to run Trimmomatic jar file as a Galaxy tool
+echo Arguments:
+for i in $@ ; do
+    echo "*" $i
+done
+
+if [ -n "$CONDA_PREFIX" ] ; then
+  # bioconda installs trimmomatic in a share directory
+  # with a jarfile called trimmomatic.jar
+  TRIMMOMATIC_DIR="$CONDA_PREFIX/share/trimmomatic"
+  JARFILE="trimmomatic.jar"
+else
+  JARFILE="trimmomatic-0.36.jar"
+fi
+
+if [ -z "$TRIMMOMATIC_DIR" ] ; then
+  echo "TRIMMOMATIC_DIR variable not set, can't find jar file"
+  exit 1
+fi
+
+java -mx8G -jar $TRIMMOMATIC_DIR/$JARFILE $@ 2>&1 | tee trimmomatic.log
+status=$?
+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 d8975856862e trimmomatic.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/trimmomatic.xml	Fri Jan 20 08:00:23 2017 -0500
@@ -0,0 +1,434 @@
+<tool id="trimmomatic" name="Trimmomatic" version="0.36.1">
+  <description>flexible read trimming tool for Illumina NGS data</description>
+  <requirements>
+    <requirement type="package" version="0.36">trimmomatic</requirement>
+  </requirements>
+  <stdio>
+    <exit_code range="1:" />
+  </stdio>
+  <command><![CDATA[
+  #if $paired_end.is_paired_end
+    #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type
+    #if $paired_input_type == "pair_of_files"
+      #set r1_ext = $paired_end.paired_input_type_conditional.fastq_r1_in.extension
+      #set r2_ext = $paired_end.paired_input_type_conditional.fastq_r2_in.extension
+      ln -s '${paired_end.paired_input_type_conditional.fastq_r1_in}' fastq_r1.'$r1_ext' &&
+      ln -s '${paired_end.paired_input_type_conditional.fastq_r2_in}' fastq_r2.'$r2_ext' &&
+    #else
+      #set r1_ext = $paired_end.paired_input_type_conditional.fastq_pair.forward.extension
+      #set r2_ext = $paired_end.paired_input_type_conditional.fastq_pair.reverse.extension
+      ln -s '${paired_end.paired_input_type_conditional.fastq_pair.forward}' fastq_r1.'$r1_ext' &&
+      ln -s '${paired_end.paired_input_type_conditional.fastq_pair.reverse}' fastq_r2.'$r2_ext' &&
+    #end if
+  #else
+      ln -s '$fastq_in' fastq_in.'$fastq_in.extension' &&
+  #end if
+  bash '${__tool_directory__}/trimmomatic.sh'
+  #if $paired_end.is_paired_end
+    PE -threads \${GALAXY_SLOTS:-6} -phred33
+      fastq_r1.'$r1_ext' fastq_r2.'$r2_ext'
+      fastq_out_r1_paired.'$r1_ext' fastq_out_r1_unpaired.'$r1_ext'
+      fastq_out_r2_paired.'$r2_ext' fastq_out_r2_unpaired.'$r2_ext'
+  #else
+    SE -threads \${GALAXY_SLOTS:-6} -phred33 fastq_in.'$fastq_in.extension' fastq_out.'$fastq_in.extension'
+  #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
+    #if str( $op.operation.name ) == "AVGQUAL"
+      AVGQUAL:$op.operation.avgqual
+    #end if
+    #if str( $op.operation.name ) == "MAXINFO"
+      MAXINFO:$op.operation.target_length:$op.operation.strictness
+    #end if
+  #end for
+  &&
+  #if $paired_end.is_paired_end
+    #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type
+    #if $paired_input_type == "pair_of_files"
+      mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_r1_paired}' &&
+      mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_r1_unpaired}' &&
+      mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_r2_paired}' &&
+      mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_r2_unpaired}'
+    #else
+      mv fastq_out_r1_paired.'$r1_ext' '${fastq_out_paired.forward}' &&
+      mv fastq_out_r1_unpaired.'$r1_ext' '${fastq_out_unpaired.forward}' &&
+      mv fastq_out_r2_paired.'$r2_ext' '${fastq_out_paired.reverse}' &&
+      mv fastq_out_r2_unpaired.'$r2_ext' '${fastq_out_unpaired.reverse}'
+    #end if
+  #else
+    mv fastq_out.'$fastq_in.extension' '${fastq_out}'
+  #end if
+  ]]></command>
+  <inputs>
+    <conditional name="paired_end">
+    <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="True" />
+    <when value="no">
+      <param name="fastq_in" type="data" format="fastqsanger|fastqsanger.gz" label="Input FASTQ file" />
+    </when>
+    <when value="yes">
+      <conditional name="paired_input_type_conditional">
+        <param name="paired_input_type" type="select" label="Input Type">
+          <option value="pair_of_files" selected="true">Pair of datasets</option>
+          <option value="collection">Dataset collection pair</option>
+        </param>
+        <when value="pair_of_files">
+ 	  <param name="fastq_r1_in" type="data" format="fastqsanger|fastqsanger.gz"
+		 label="Input FASTQ file (R1/first of pair)" />
+ 	  <param name="fastq_r2_in" type="data" format="fastqsanger|fastqgsanger.gz"
+		 label="Input FASTQ file (R2/second of pair)" />
+	</when>
+        <when value="collection">
+          <param name="fastq_pair" format="fastqsanger|fastqsanger.gz" type="data_collection"
+ 		 collection_type="paired"
+ 		 label="Select FASTQ dataset collection with R1/R2 pair" />
+        </when>
+      </conditional>
+    </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="False" />
+    <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>
+    <when value="no" /> <!-- empty clause to satisfy planemo lint -->
+    </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>
+	  <option value="AVGQUAL">Drop reads with average quality lower than a specified level (AVGQUAL)</option>
+	  <option value="MAXINFO">Trim reads adaptively, balancing read length and error rate to maximise the value of each read (MAXINFO)</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>
+	<when value="AVGQUAL">
+	  <param name="avgqual" type="integer" label="Minimum average quality required to keep a read" value="" />
+	</when>
+	<when value="MAXINFO">
+	  <param name="target_length" type="integer" label="Target read length" value="" help="The read length which is likely to allow the location of the read within the target sequence to be determined." />
+	  <param name="strictness" type="float" label="Strictness" value="" help="Set between zero and one - specifies the balance between preserving read length versus removal of incorrect bases; low values (&lt;0.2) favours longer reads, high values (&gt;0.8) favours read correctness." />
+	</when>
+      </conditional>
+    </repeat>
+  </inputs>
+  <outputs>
+    <data name="fastq_out_r1_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 paired)"
+      format_source="${paired_end.paired_input_type_conditional.fastq_r1_in}">
+      <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
+    </data>
+    <data name="fastq_out_r2_paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 paired)"
+      format_source="${paired_end.paired_input_type_conditional.fastq_r2_in}">
+      <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
+    </data>
+    <data name="fastq_out_r1_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r1_in.name} (R1 unpaired)"
+      format_source="${paired_end.paired_input_type_conditional.fastq_r1_in}">
+      <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
+    </data>
+    <data name="fastq_out_r2_unpaired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_r2_in.name} (R2 unpaired)"
+      format_source="${paired_end.paired_input_type_conditional.fastq_r1_in}">
+      <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "pair_of_files"</filter>
+    </data>
+    <data name="fastq_out" label="${tool.name} on ${paired_end.fastq_in.name}"
+      format_source="${fastq_in}">
+      <filter>not paired_end['is_paired_end']</filter>
+    </data>
+    <collection name="fastq_out_paired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: paired">
+      <data name="forward" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 paired)"
+        format_source="${paired_end.paired_input_type_conditional.fastq_pair.forward}" />
+      <data name="reverse" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 paired)"
+        format_source="${paired_end.paired_input_type_conditional.fastq_pair.reverse}" />
+      <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter>
+    </collection>
+    <collection name="fastq_out_unpaired" type="paired" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.name}: unpaired">
+      <data name="forward" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.forward.name} (R1 unpaired)"
+        format_source="${paired_end.paired_input_type_conditional.fastq_pair.forward}" />
+      <data name="reverse" label="${tool.name} on ${paired_end.paired_input_type_conditional.fastq_pair.reverse.name} (R2 unpaired)"
+        format_source="${paired_end.paired_input_type_conditional.fastq_pair.reverse}" />
+      <filter>paired_end['is_paired_end']</filter>
+      <filter>paired_end['paired_input_type_conditional']['paired_input_type'] == "collection"</filter>
+    </collection>
+  </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>
+      <!-- Single-end example - gzipped -->
+      <param name="is_paired_end" value="no" />
+      <param name="fastq_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
+      <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.gz" />
+    </test>
+    <test>
+      <!-- Paired-end example - gzipped -->
+      <param name="is_paired_end" value="yes" />
+      <param name="fastq_r1_in" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
+      <param name="fastq_r2_in" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz" />
+      <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.gz" />
+      <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
+      <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
+      <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
+    </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>
+    <test>
+      <!-- Paired-end with dataset collection -->
+      <param name="is_paired_end" value="yes" />
+      <param name="paired_input_type" value="collection" />
+      <param name="fastq_pair">
+        <collection type="paired">
+          <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />
+          <element name="reverse" value="Illumina_SG_R2.fastq" ftype="fastqsanger"/>
+        </collection>
+      </param>
+      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
+      <output_collection name="fastq_out_paired" type="paired">
+    <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" />
+    <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" />
+      </output_collection>
+      <output_collection name="fastq_out_unpaired" type="paired">
+    <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" />
+    <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
+      </output_collection>
+    </test>
+    <test>
+      <!-- Paired-end with dataset collection - gzipped -->
+      <param name="is_paired_end" value="yes" />
+      <param name="paired_input_type" value="collection" />
+      <param name="fastq_pair">
+        <collection type="paired">
+          <element name="forward" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />
+          <element name="reverse" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz"/>
+        </collection>
+      </param>
+      <param name="operations_0|operation|name" value="SLIDINGWINDOW" />
+      <output_collection name="fastq_out_paired" type="paired">
+    <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq.gz" />
+    <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />
+      </output_collection>
+      <output_collection name="fastq_out_unpaired" type="paired">
+    <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />
+    <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />
+      </output_collection>
+    </test>
+    <test>
+      <!-- Single-end using AVGQUAL -->
+      <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="AVGQUAL" />
+      <param name="operations_0|operation|avgqual" value="30" />
+      <output name="fastq_out" file="trimmomatic_avgqual.fastq" />
+    </test>
+    <test>
+      <!-- Single-end using MAXINFO -->
+      <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="MAXINFO" />
+      <param name="operations_0|operation|target_length" value="75" />
+      <param name="operations_0|operation|strictness" value="0.8" />
+      <output name="fastq_out" file="trimmomatic_maxinfo.fastq" />
+    </test>
+  </tests>
+  <help><![CDATA[
+.. 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
+ * **AVGQUAL:** Drop the read if the average quality is below a specified value
+ * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to
+   maximise the value of each 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
+
+**Inputs**
+
+For single-end data this Trimmomatic tool accepts a single FASTQ file; for
+paired-end data it will accept either two FASTQ files (R1 and R2), or a
+dataset collection containing the R1/R2 FASTQ pair.
+
+.. 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.
+
+.. class:: warningmark
+
+If the input consists of a dataset collection with the R1/R2 FASTQ pair then
+the outputs will also inclue two dataset collections: one for the 'paired'
+outputs and one for the 'unpaired' (as described above)
+
+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:
+
+ * Bolger, A.M., Lohse, M., &amp; Usadel, B. (2014). Trimmomatic: A flexible trimmer
+   for Illumina Sequence Data. Bioinformatics, btu170.
+
+Please kindly acknowledge both this Galaxy tool and the Trimmomatic program if you
+use it.
+  ]]></help>
+  <citations>
+    <!--
+    See https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Ccitations.3E_tag_set
+    Can be either DOI or Bibtex
+    Use http://www.bioinformatics.org/texmed/ to convert PubMed to Bibtex
+    -->
+    <citation type="doi">10.1093/bioinformatics/btu170</citation>
+  </citations>
+</tool>