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changeset 4:14d05f2d511d draft

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Version that supports Trimmomatic 0.36.
author pjbriggs
date Thu, 14 Jul 2016 09:17:38 -0400
parents f8a9a5eaca8a
children f80107cdc406
files README.rst install_tool_deps.sh package_trimmomatic.sh run_planemo_tests.sh test-data/trimmomatic_avgqual.fastq test-data/trimmomatic_maxinfo.fastq test-data/trimmomatic_r1_paired_maxinfo.fastq test-data/trimmomatic_r1_unpaired_maxinfo.fastq test-data/trimmomatic_r2_paired_maxinfo.fastq test-data/trimmomatic_r2_unpaired_maxinfo.fastq tool_dependencies.xml trimmomatic.xml
diffstat 10 files changed, 183 insertions(+), 112 deletions(-) [+]
line wrap: on
line diff
--- a/README.rst	Wed Sep 23 08:59:23 2015 -0400
+++ b/README.rst	Thu Jul 14 09:17:38 2016 -0400
@@ -33,15 +33,15 @@
 
     <tool file="trimmomatic/trimmomatic.xml" />
 
-You will also need to install trimmomatic 0.32:
+You will also need to install trimmomatic 0.36:
 
-- http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
+- 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-0.32.jar`` file
+  ``trimmomatic-0.36.jar`` file
 - ``TRIMMOMATIC_ADAPTERS_DIR`` should point to the directory holding the adapter
   sequence files (used by the ``ILLUMINACLIP`` option).
 
@@ -58,6 +58,8 @@
 ========== ======================================================================
 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.
--- a/install_tool_deps.sh	Wed Sep 23 08:59:23 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,40 +0,0 @@
-#!/bin/bash
-#
-# Install dependencies for Trimmomatic for testing from the command line
-#
-# 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
-cd $TOP_DIR
-# Trimmomatic 0.32
-INSTALL_DIR=$TOP_DIR/trimmomatic/0.32
-mkdir -p $INSTALL_DIR
-wd=$(mktemp -d)
-pushd $wd
-wget -q http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.32.zip
-unzip -qq Trimmomatic-0.32.zip
-mv Trimmomatic-0.32/trimmomatic-0.32.jar $INSTALL_DIR/
-mv Trimmomatic-0.32/adapters/ $INSTALL_DIR/
-popd
-rm -rf $wd/*
-rmdir $wd
-# Make setup file
-cat > trimmomatic/0.32/env.sh <<EOF
-#!/bin/sh
-# Source this to setup trimmomatic/0.32
-echo Setting up Trimmomatic 0.32
-export TRIMMOMATIC_DIR=$INSTALL_DIR
-export TRIMMOMATIC_ADAPTERS_DIR=$INSTALL_DIR/adapters
-#
-EOF
-##
-#
--- a/package_trimmomatic.sh	Wed Sep 23 08:59:23 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,24 +0,0 @@
-#!/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 $TGZ >&2
-    exit 1
-fi
-##
-#
--- a/run_planemo_tests.sh	Wed Sep 23 08:59:23 2015 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,39 +0,0 @@
-#!/bin/bash
-#
-# Install dependencies and set up environment for
-# trimmomatic tool, then run tests using planemo
-#
-# Note that any arguments supplied to the script are
-# passed directly to the "planemo test..." invocation
-#
-# e.g. --install_galaxy (to get planemo to create a
-#                        Galaxy instance to run tests)
-#
-#      --galaxy_root DIR (to run tests using existing
-#                         Galaxy instance)
-#
-# List of dependencies
-TOOL_DEPENDENCIES="trimmomatic/0.32"
-# Where to find them
-TOOL_DEPENDENCIES_DIR=$(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
-##
-#
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_avgqual.fastq	Thu Jul 14 09:17:38 2016 -0400
@@ -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#########
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_maxinfo.fastq	Thu Jul 14 09:17:38 2016 -0400
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_r1_paired_maxinfo.fastq	Thu Jul 14 09:17:38 2016 -0400
@@ -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
+GAGCAGTCGGGCTCAGCGCTNTGCAAATTCTAGTTAGAAACTCACAGTTCTGACAAGCCTTAGGTCAGTG
++
+5====>/<@@@@@@>@CCCE#66>ACEEEEGGGGGGGFFFEFDFFFFF=CDEFFFFEDEFFFFFC=AEBF
+@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
+GTGCAGGGGGTGTGGTCAATCCACACTGTTGCTGAGGTGATTGGGTCTCCGGGGTCAACTCCA
++
+=5===<>+5<5<+5=@CC;8CEEEEE;-8ACFDE.7C87CF-A>E>E=FFE**>>5AEDAEED
+@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 1:N:0:TAAGGCGATAGATCGC
+TCTCAGATGAGCATGCAGCAGCCCAGACTCGCCCCACGCAGTTTGCCAACCACAAG
++
+=,,<=>>>@@@@@9@@CCEE@EE+++6C8-++CECE+>DCC>@@EFFFFEEEDEE5
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/trimmomatic_r2_paired_maxinfo.fastq	Thu Jul 14 09:17:38 2016 -0400
@@ -0,0 +1,40 @@
+@MISEQ:1:000000000-A2Y1L:1:1101:19264:2433 2:N:0:NAAGGCGATAGATCGC
+GCCGATATGCAGATGCCGTTGATTGCTGCCAGCATAGCAGCCATTGCCGGCATATCCTTTGTGACTGTGCGCCGACGCAAGAAGGCGGCCCAGATAACCTAGCCCAGAAACG
++
+??A??ABBDDDDDDDDFFEEEFHIIIIHHIIHIFHIIHHHFHHIIIIIHHHFHHIIIIIIFFFHHIIHGDEHHAAEHHHHFHHHHD=EBBEEEEEFFFFEEEECEFFEEFFF
+@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
+GTCCACGTGAAATCCCGAGCGTCCCTCTCCCTCCCGAGAACCCGGTCTATATCCCACGATTTTTG
++
+????9B???AD9?BDDEEDDDDHHHHHFHFHFFHHHHHHHHHEHH>CEGHHFGHHGHH=FHHHHC
+@MISEQ:1:000000000-A2Y1L:1:1101:18851:2442 2:N:0:NAAGGCGATAGATCGC
+TCTCCTCAGTACGGGGGAGGAGGTTCGCTCGGCGGACGTGCGGCCCTACGCCAGACTCTACCACATGGTTCAGCAGGAGCTGGAGCACCGCGCTGTGTCCGGGGACTGGGAATACACCATCAGCCCCGGCGAGGAGTGGCAAGAGA
++
+A??A?BBBDDDDDDDDGGGGGGHEFHHGEHHHIHEHHHHHDHBEHGFFFEGGDEEDGGGGGEGGEECE?EGCEGEGGGCEEEGGCEEGG4D;;4AGGGGGG8>GGA?EGGGEEGEEGGGCGGEGEGGGGD8<AADECECEGG?CCC
+@MISEQ:1:000000000-A2Y1L:1:1101:15290:2442 2:N:0:NAAGGCGATAGATCGC
+GCGTGGATTTGATTCGGTTTATGGGGCGCGGCCGCTGAGGCGGGTCATTCAGACGGAG
++
+?????@?BDDDDDDDDFEEEFFHIIHEHHHHDHHHHHEHHHHHH8ADFFFDFFD1D;>
+@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC
+GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCT
++
+?????BBBDDDDDDDDGCFGFGIIIIIHFHIIIIHIHFG=EHHIGIIIIFHIHDGHGHHHIHIH=CGHGGHFHHHFHFGHHFH/ACDFGG?FE?CDFFHHHHHIIHFHHI>CEDGFHHHHHHHHDFHHFHHHFFAFFGGGGGGEDEG>>DACC;?EGG>CEEA>AEACCEE?
+@MISEQ:1:000000000-A2Y1L:1:1101:15892:2446 2:N:0:NAAGGCGATAGATCGC
+GTATTGCTGGCACCATCAGTCACCGTGTAGTGTATTCTATCGATTCCGTCACGCTGGCCCTTGAGCGTGCCCGAATCATACGTTATGGTGGTACCTGATACCGTGGCACTAGTGCCGTCGGTGTCTGCGCCATCCG
++
+?????BBBDDDDDDDDGGGGGGIIHIIFHHHIHHIFHGHGGHHIHIIDEFFHEF@DFHIIHIIIGHACDCFFHHHIHIIHIHGHHHBGFGEEHHHHFHFFHHDFDCEGGFGGFGGG@DBEEEEGC>CEEGGGGGGE
+@MISEQ:1:000000000-A2Y1L:1:1101:17903:2450 2:N:0:TAAGGCGATAGATCGC
+GGCCAACACTGTGGTCACTATCTCTGGCACTGGTCTGCTACCACATGGAGTTGACACCGGAGACCCAATCACCACAGCAACAGTGTGGATTGACCACACCCCCTGCACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGA
++
+55<?????DDDBBDDBFFFFFFCHHIIHHIIIIIIIHGHHIIIIHHGHIIHFHHIIIIHHHCDHIIIHFFHIIIIICFFHIHECGCGEHIH=FHHHHHHHHHHF;FFFFFDDFFFFFFFEFFFFEFEBDFAEEAEE@EEDD>DDD
+@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC
+GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAGAGGAGGAGGAGAGA
++
+?????@9@B?B?BBBBEEEFB@@EEHEC?BF-CE@DDEH,5+5C,>@+CE+<?=E
--- a/tool_dependencies.xml	Wed Sep 23 08:59:23 2015 -0400
+++ b/tool_dependencies.xml	Thu Jul 14 09:17:38 2016 -0400
@@ -1,11 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="trimmomatic" version="0.32">
+    <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-0.32.zip</action>
+	  <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip</action>
 	  <action type="move_file">
-	    <source>trimmomatic-0.32.jar</source>
+	    <source>trimmomatic-0.36.jar</source>
 	    <destination>$INSTALL_DIR</destination>
 	  </action>
           <action type="move_directory_files">
--- a/trimmomatic.xml	Wed Sep 23 08:59:23 2015 -0400
+++ b/trimmomatic.xml	Thu Jul 14 09:17:38 2016 -0400
@@ -1,7 +1,7 @@
-<tool id="trimmomatic" name="Trimmomatic" version="0.32.3">
+<tool id="trimmomatic" name="Trimmomatic" version="0.36.0">
   <description>flexible read trimming tool for Illumina NGS data</description>
   <requirements>
-    <requirement type="package" version="0.32">trimmomatic</requirement>
+    <requirement type="package" version="0.36">trimmomatic</requirement>
   </requirements>
   <stdio>
     <exit_code range="1:" />
@@ -9,7 +9,7 @@
   <command interpreter="bash"><![CDATA[
   trimmomatic.sh
   -mx8G
-  -jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar
+  -jar \$TRIMMOMATIC_DIR/trimmomatic-0.36.jar
   #if $paired_end.is_paired_end
     PE -threads \${GALAXY_SLOTS:-6} -phred33
     #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type
@@ -53,6 +53,12 @@
     #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
   ]]></command>
   <inputs>
@@ -96,6 +102,7 @@
       <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">
@@ -106,6 +113,8 @@
 	  <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" />
@@ -126,6 +135,13 @@
 	<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>
@@ -224,6 +240,23 @@
 	<element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />
       </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
@@ -243,6 +276,9 @@
  * **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