| Previous changeset 3:f8a9a5eaca8a (2015-09-23) Next changeset 5:f80107cdc406 (2016-12-16) |
|
Commit message:
Version that supports Trimmomatic 0.36. |
|
modified:
README.rst tool_dependencies.xml trimmomatic.xml |
|
added:
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 |
|
removed:
install_tool_deps.sh package_trimmomatic.sh run_planemo_tests.sh |
| b |
| diff -r f8a9a5eaca8a -r 14d05f2d511d README.rst --- a/README.rst Wed Sep 23 08:59:23 2015 -0400 +++ b/README.rst Thu Jul 14 09:17:38 2016 -0400 |
| b |
| @@ -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. |
| b |
| diff -r f8a9a5eaca8a -r 14d05f2d511d install_tool_deps.sh --- 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 -## -# |
| b |
| diff -r f8a9a5eaca8a -r 14d05f2d511d package_trimmomatic.sh --- 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 $TGZ >&2 - exit 1 -fi -## -# |
| b |
| diff -r f8a9a5eaca8a -r 14d05f2d511d run_planemo_tests.sh --- a/run_planemo_tests.sh Wed Sep 23 08:59:23 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,39 +0,0 @@ -#!/bin/bash -# -# Install dependencies and set up environment for -# trimmomatic tool, then run tests using planemo -# -# Note that any arguments supplied to the script are -# passed directly to the "planemo test..." invocation -# -# e.g. --install_galaxy (to get planemo to create a -# Galaxy instance to run tests) -# -# --galaxy_root DIR (to run tests using existing -# Galaxy instance) -# -# List of dependencies -TOOL_DEPENDENCIES="trimmomatic/0.32" -# Where to find them -TOOL_DEPENDENCIES_DIR=$(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 -## -# |
| b |
| diff -r f8a9a5eaca8a -r 14d05f2d511d test-data/trimmomatic_avgqual.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_avgqual.fastq Thu Jul 14 09:17:38 2016 -0400 |
| b |
| @@ -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######### |
| b |
| diff -r f8a9a5eaca8a -r 14d05f2d511d test-data/trimmomatic_maxinfo.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_maxinfo.fastq Thu Jul 14 09:17:38 2016 -0400 |
| b |
| @@ -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 |
| b |
| diff -r f8a9a5eaca8a -r 14d05f2d511d test-data/trimmomatic_r1_paired_maxinfo.fastq --- /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 |
| b |
| @@ -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 |
| b |
| diff -r f8a9a5eaca8a -r 14d05f2d511d test-data/trimmomatic_r2_paired_maxinfo.fastq --- /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 |
| b |
| @@ -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 |
| b |
| diff -r f8a9a5eaca8a -r 14d05f2d511d tool_dependencies.xml --- a/tool_dependencies.xml Wed Sep 23 08:59:23 2015 -0400 +++ b/tool_dependencies.xml Thu Jul 14 09:17:38 2016 -0400 |
| b |
| @@ -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"> |
| b |
| diff -r f8a9a5eaca8a -r 14d05f2d511d trimmomatic.xml --- 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 (<0.2) favours longer reads, high values (>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 |