| Previous changeset 4:14d05f2d511d (2016-07-14) Next changeset 6:141bba0e9a77 (2017-02-24) |
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Commit message:
Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now). |
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modified:
README.rst tool_dependencies.xml trimmomatic.xml |
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added:
trimmomatic_macros.xml |
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removed:
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 trimmomatic.sh |
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| diff -r 14d05f2d511d -r f80107cdc406 README.rst --- a/README.rst Thu Jul 14 09:17:38 2016 -0400 +++ b/README.rst Fri Dec 16 11:31:55 2016 -0500 |
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| @@ -58,6 +58,8 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +0.36.1 - Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version + is still supported for now). 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 |
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| diff -r 14d05f2d511d -r f80107cdc406 test-data/trimmomatic_r1_paired_maxinfo.fastq --- a/test-data/trimmomatic_r1_paired_maxinfo.fastq Thu Jul 14 09:17:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,40 +0,0 @@ -@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 |
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| diff -r 14d05f2d511d -r f80107cdc406 test-data/trimmomatic_r2_paired_maxinfo.fastq --- a/test-data/trimmomatic_r2_paired_maxinfo.fastq Thu Jul 14 09:17:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,40 +0,0 @@ -@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 |
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| diff -r 14d05f2d511d -r f80107cdc406 tool_dependencies.xml --- a/tool_dependencies.xml Thu Jul 14 09:17:38 2016 -0400 +++ b/tool_dependencies.xml Fri Dec 16 11:31:55 2016 -0500 |
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| @@ -4,7 +4,7 @@ <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"> + <action type="move_file" rename_to="trimmomatic.jar"> <source>trimmomatic-0.36.jar</source> <destination>$INSTALL_DIR</destination> </action> @@ -13,10 +13,10 @@ <destination_directory>$INSTALL_DIR/adapters</destination_directory> </action> <action type="set_environment"> - <environment_variable name="TRIMMOMATIC_DIR" action="set_to">$INSTALL_DIR</environment_variable> + <environment_variable name="TRIMMOMATIC_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable> </action> <action type="set_environment"> - <environment_variable name="TRIMMOMATIC_ADAPTERS_DIR" action="set_to">$INSTALL_DIR/adapters</environment_variable> + <environment_variable name="TRIMMOMATIC_ADAPTERS_PATH" action="set_to">$INSTALL_DIR/adapters</environment_variable> </action> </actions> </install> |
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| diff -r 14d05f2d511d -r f80107cdc406 trimmomatic.sh --- a/trimmomatic.sh Thu Jul 14 09:17:38 2016 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,18 +0,0 @@ -#!/bin/sh -# -# Shell wrapper to run Trimmomatic jar file as a Galaxy tool -echo Arguments: -for i in $@ ; do - echo "*" $i -done -java $@ 2>&1 | tee trimmomatic.log -status=$? -echo "Exit status: $status" -# Check for successful completion -if [ -z "$(tail -1 trimmomatic.log | grep "Completed successfully")" ] ; then - echo "Trimmomatic did not finish successfully" >&2 - exit 1 -fi -exit $status -## -# |
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| diff -r 14d05f2d511d -r f80107cdc406 trimmomatic.xml --- a/trimmomatic.xml Thu Jul 14 09:17:38 2016 -0400 +++ b/trimmomatic.xml Fri Dec 16 11:31:55 2016 -0500 |
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| @@ -1,15 +1,18 @@ -<tool id="trimmomatic" name="Trimmomatic" version="0.36.0"> +<tool id="trimmomatic" name="Trimmomatic" version="0.36.1"> <description>flexible read trimming tool for Illumina NGS data</description> + <macros> + <import>trimmomatic_macros.xml</import> + </macros> <requirements> <requirement type="package" version="0.36">trimmomatic</requirement> </requirements> <stdio> <exit_code range="1:" /> </stdio> - <command interpreter="bash"><![CDATA[ - trimmomatic.sh - -mx8G - -jar \$TRIMMOMATIC_DIR/trimmomatic-0.36.jar + <command><![CDATA[ + @CONDA_TRIMMOMATIC_JAR_PATH@ && + @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ && + java -mx8G -jar \$TRIMMOMATIC_JAR_PATH/trimmomatic.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 @@ -29,7 +32,7 @@ #end if ## ILLUMINACLIP option #if $illuminaclip.do_illuminaclip - ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_DIR/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold + ILLUMINACLIP:\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold #end if ## Other operations #for $op in $operations @@ -60,6 +63,8 @@ MAXINFO:$op.operation.target_length:$op.operation.strictness #end if #end for + 2>&1 | tee trimmomatic.log && + if [ -z "\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi ]]></command> <inputs> <conditional name="paired_end"> |
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| diff -r 14d05f2d511d -r f80107cdc406 trimmomatic_macros.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trimmomatic_macros.xml Fri Dec 16 11:31:55 2016 -0500 |
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| @@ -0,0 +1,8 @@ +<macros> + <!-- + Set the path for the trimmomatic JAR and data files + Based on https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/snpsift/snpSift_macros.xml#L13 + --> + <token name="@CONDA_TRIMMOMATIC_JAR_PATH@">if [ -z "\$TRIMMOMATIC_JAR_PATH" ]; then export TRIMMOMATIC_JAR_PATH=\$(dirname \$(readlink -e \$(which trimmomatic))); fi</token> + <token name="@CONDA_TRIMMOMATIC_ADAPTERS_PATH@">if [ -z "\$TRIMMOMATIC_ADAPTERS_PATH" ]; then export TRIMMOMATIC_ADAPTERS_PATH=\$(dirname \$(readlink -e \$(which trimmomatic)))/adapters; fi</token> +</macros> |