| Previous changeset 7:6eeacf19a38e (2017-03-21) Next changeset 9:53af7b5b1b56 (2017-08-21) |
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Commit message:
Uploaded v0.36.4. |
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modified:
README.rst trimmomatic.xml |
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added:
test-data/trimmomatic_pe_r1_paired_out1_clip.fastq test-data/trimmomatic_pe_r2_unpaired_out1_clip.fastq |
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| diff -r 6eeacf19a38e -r 415a165d92bb README.rst --- a/README.rst Tue Mar 21 08:42:05 2017 -0400 +++ b/README.rst Thu Jun 22 09:07:16 2017 -0400 |
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| @@ -71,6 +71,9 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +0.36.4 - Add option to provide custom adapter sequences for ILLUMINACLIP + - Add options ``minAdapterLength`` and ``keepBothReads`` for ILLUMINACLIP + in palindrome mode 0.36.3 - Fix naming of output collections. Instead of all outputs being called "Trimmomatic on collection NN" these will now be called "Trimmomatic on collection NN: paired" or "Trimmomatic on collection NN: unpaired". @@ -106,7 +109,8 @@ This wrapper has been developed and is maintained by Peter Briggs (@pjbriggs). Peter van Heusden (@pvanheus) and Marius van den Beek (@mvdbeek) contributed -support for gz compressed FastQ files. +support for gz compressed FastQ files. Charles Girardot (@cgirardot) and +Jelle Scholtalbers (@scholtalbers) contributed additional options to ILLUMINACLIP. Developers |
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| diff -r 6eeacf19a38e -r 415a165d92bb test-data/trimmomatic_pe_r1_paired_out1_clip.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_pe_r1_paired_out1_clip.fastq Thu Jun 22 09:07:16 2017 -0400 |
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| @@ -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 +AAAATAATCCTAAAAAATAACCTCTATGCCGCCGAACGCTCCGCCTCTATCTTCGTAAAAACTATCTTCTCCTCCTCACCTCCATAATCAAGCATCAAGCGATCGCCCTCCGCCAACTCACCCCGCAAAATCTTATCCGCTAGCGGATTCTCAATCTCCGTCTGAATGACCCGCCTCAGCGGCCGCGCCCCATAAACCGAATCAAATCCACGC ++ +?????BBBDDDDDDDDGGGGGGIIIHHFFHHHHHHHHHHEHHEHHHHHIIHHHHHFEHIIIHHIHHIHIHIIIIIHHHHHHHHHHHHHHHHDHHHHHHHHGEDFGGGGGGG;CEGEGCEGGGGG8>GGGGEGGEECEGGGGD8EDGGAEGEEGGCE:CGG8CEEGG???CEE<DG8CC*??>DG.8<AGGGGCEEG*C2<GCCECE*:?CE?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< |
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| diff -r 6eeacf19a38e -r 415a165d92bb test-data/trimmomatic_pe_r2_unpaired_out1_clip.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/trimmomatic_pe_r2_unpaired_out1_clip.fastq Thu Jun 22 09:07:16 2017 -0400 |
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| @@ -0,0 +1,8 @@ +@MISEQ:1:000000000-A2Y1L:1:1101:18106:2444 2:N:0:NAAGGCGATAGATCGC +GAGTTACTATTACAGAGTGGAGCTAATGTACTGGCAGTTGACTGCAAAAGAAATGCTCCAATTCATGTTGCATGTGCAAATATGAGCTTAGAGTGTTTAAAGATAATTTTGTGCCACAAAAAATGCAACCCAAACCAACAAAATGCAGTGGGAGACACTCCACTCCACACCTTATGCAGTTTGGGGACTTGTGATATGAGAATACTAC ++ +?????BBBDDDDDDDDGCFGFGIIIIIHFHIIIIHIHFG=EHHIGIIIIFHIHDGHGHHHIHIH=CGHGGHFHHHFHFGHHFH/ACDFGG?FE?CDFFHHHHHIIHFHHI>CEDGFHHHHHHHHDFHHFHHHFFAFFGGGGGGEDEG>>DACC;?EGG>CEEA>AEACCEE?:C::CC:::C:CE<C<9C:?C?*?CEECCC*:C?C? +@MISEQ:1:000000000-A2Y1L:1:1101:15113:2451 2:N:0:TAAGGCGATAGATCGC +GAGGGGAGGAGGGGAAGGGAGAGGGGAAGAGAGGAGAGGAG ++ +?????@9@B?B?BBBBEEEFB@@EEHEC?BF-CE@DDEH,5 |
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| diff -r 6eeacf19a38e -r 415a165d92bb trimmomatic.xml --- a/trimmomatic.xml Tue Mar 21 08:42:05 2017 -0400 +++ b/trimmomatic.xml Thu Jun 22 09:07:16 2017 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="trimmomatic" name="Trimmomatic" version="0.36.3">\n+<tool id="trimmomatic" name="Trimmomatic" version="0.36.4">\n <description>flexible read trimming tool for Illumina NGS data</description>\n <macros>\n <import>trimmomatic_macros.xml</import>\n@@ -33,7 +33,19 @@\n #end if\n ## ILLUMINACLIP option\n #if $illuminaclip.do_illuminaclip\n- ILLUMINACLIP:\\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold\n+ #if $illuminaclip.adapter_type.standard_or_custom == "custom"\n+ #if $readtype.single_or_paired in ["pair_of_files","collection"]\n+ ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads\n+ #else\n+ ILLUMINACLIP:$adapter_file_from_text:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold\n+ #end if\n+ #else\n+ #if $readtype.single_or_paired in ["pair_of_files","collection"]\n+ ILLUMINACLIP:\\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_type.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold:$illuminaclip.min_adapter_len:$illuminaclip.keep_both_reads\n+ #else\n+ ILLUMINACLIP:\\$TRIMMOMATIC_ADAPTERS_PATH/$illuminaclip.adapter_type.adapter_fasta:$illuminaclip.seed_mismatches:$illuminaclip.palindrome_clip_threshold:$illuminaclip.simple_clip_threshold\n+ #end if\n+ #end if\n #end if\n ## Other operations\n #for $op in $operations\n@@ -81,6 +93,14 @@\n mv fastq_out.\'$fastq_in.extension\' \'${fastq_out}\'\n #end if\n ]]></command>\n+ <configfiles>\n+ <configfile name="adapter_file_from_text">#set from_text_area = \'\'\n+#if str( $illuminaclip.do_illuminaclip ) == "yes" and str( $illuminaclip.adapter_type.standard_or_custom ) == "custom":\n+#set from_text_area = $illuminaclip.adapter_type.adapter_text\n+#end if\n+${from_text_area}</configfile>\n+ </configfiles>\n+\n <inputs>\n <conditional name="readtype">\n <param name="single_or_paired" type="select" label="Single-end or paired-end reads?">\n@@ -104,17 +124,37 @@\n <conditional name="illuminaclip">\n <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" />\n <when value="yes">\n- <param name="adapter_fasta" type="select" label="Adapter sequences to use">\n- <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>\n- <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>\n- <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>\n- <option value="TruSeq3-PE.fa">TruSeq3 (paired-ended, for MiSeq and HiSeq)</option>\n- <option value="TruSeq3-PE-2.fa">TruSeq3 (additional seqs) (paired-ended, for MiSeq and HiSeq)</option>\n- <option value="NexteraPE-PE.fa">Nextera (paired-ended)</option>\n- </param>\n+ <conditional name="adapter_type">\n+ <param name="standard_or_custom" type="select" label="Select standard adapter sequences or provide custom?">\n+ <option value="standard" selected="true">Standard</option>\n+ <option value="custom">Custom</option>\n+ </param>\n+ <when value="standard">\n+ <param name="adapter_fasta" type="select" label="Adapter sequences to use">\n+ <option value="TruSeq2-SE.fa">TruSeq2 (single-ended, for Illumina GAII)</option>\n+ <option value="TruSeq3-SE.fa">TruSeq3 (single-ended, for MiSeq and HiSeq)</option>\n+ <option value="TruSeq2-PE.fa">TruSeq2 (paired-ended, for Illumina GAII)</option>\n+ <'..b'stq" />\n </test>\n+ <test>\n+ <!-- Paired-end ILLUMINACLIP - this does not check valid clipping -->\n+ <param name="single_or_paired" value="pair_of_files" />\n+ <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />\n+ <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />\n+ <param name="do_illuminaclip" value="true"/>\n+ <param name="adapter_fasta" value="TruSeq2-PE.fa"/>\n+ <param name="operations_0|operation|name" value="SLIDINGWINDOW" />\n+ <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" />\n+ <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />\n+ <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />\n+ <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" />\n+ </test>\n+ <test>\n+ <!-- Paired-end ILLUMINACLIP providing \'custom\' adapters - this does not check valid clipping -->\n+ <param name="single_or_paired" value="pair_of_files" />\n+ <param name="fastq_r1_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />\n+ <param name="fastq_r2_in" value="Illumina_SG_R2.fastq" ftype="fastqsanger" />\n+ <param name="do_illuminaclip" value="true"/>\n+ <param name="standard_or_custom" value="custom"/>\n+ <param name="adapter_text"\n+ value=">PrefixPE/1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT >PrefixPE/2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT >PCR_Primer1 AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT >PCR_Primer1_rc AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT >PCR_Primer2 CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT >PCR_Primer2_rc AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG >FlowCell1 TTTTTTTTTTAATGATACGGCGACCACCGAGATCTACAC >FlowCell2 TTTTTTTTTTCAAGCAGAAGACGGCATACGA "/>\n+ <param name="adapter_fasta" value="TruSeq2-PE.fa"/>\n+ <param name="operations_0|operation|name" value="SLIDINGWINDOW" />\n+ <output name="fastq_out_r1_paired" file="trimmomatic_pe_r1_paired_out1_clip.fastq" />\n+ <output name="fastq_out_r1_unpaired" file="trimmomatic_pe_r1_unpaired_out1.fastq" />\n+ <output name="fastq_out_r2_paired" file="trimmomatic_pe_r2_paired_out1.fastq" />\n+ <output name="fastq_out_r2_unpaired" file="trimmomatic_pe_r2_unpaired_out1_clip.fastq" />\n+ </test>\n </tests>\n <help><![CDATA[\n .. class:: infomark\n@@ -299,6 +368,12 @@\n This tool allows the following trimming steps to be performed:\n \n * **ILLUMINACLIP:** Cut adapter and other illumina-specific sequences from the read\n+\n+ * If **Always keep both reads (PE specific/palindrome mode)** is True, the reverse read will also be retained in palindrome mode.\n+ After read-though has been detected by palindrome mode, and the adapter sequence removed,\n+ the reverse read contains the same sequence information as the forward read, albeit in reverse complement.\n+ For this reason, the default behaviour is to entirely drop the reverse read.\n+ Retaining the reverse read may be useful e.g. if the downstream tools cannot handle a combination of paired and unpaired reads.\n * **SLIDINGWINDOW:** Perform a sliding window trimming, cutting once the average\n quality within the window falls below a threshold\n * **MINLEN:** Drop the read if it is below a specified length\n@@ -359,8 +434,8 @@\n **Credits**\n \n This Galaxy tool has been developed within the Bioinformatics Core Facility at the\n-University of Manchester, with contributions from Peter van Heusden and Marius\n-van den Beek.\n+University of Manchester, with contributions from Peter van Heusden, Marius\n+van den Beek, Jelle Scholtalbers and Charles Girardot.\n \n It runs the Trimmomatic program which has been developed\n within Bjorn Usadel\'s group at RWTH Aachen university.\n' |