| Previous changeset 5:f80107cdc406 (2016-12-16) Next changeset 7:6eeacf19a38e (2017-03-21) |
|
Commit message:
Uploaded v0.36.2 (adds support for compressed fastq inputs) |
|
modified:
README.rst trimmomatic.xml |
|
added:
test-data/Illumina_SG_R1.fastq.gz test-data/Illumina_SG_R2.fastq.gz test-data/trimmomatic_pe_r1_paired_out1.fastq.gz test-data/trimmomatic_pe_r1_unpaired_out1.fastq.gz test-data/trimmomatic_pe_r2_paired_out1.fastq.gz test-data/trimmomatic_pe_r2_unpaired_out1.fastq.gz test-data/trimmomatic_se_out1.fastq.gz |
| b |
| diff -r f80107cdc406 -r 141bba0e9a77 README.rst --- a/README.rst Fri Dec 16 11:31:55 2016 -0500 +++ b/README.rst Fri Feb 24 05:12:32 2017 -0500 |
| b |
| @@ -58,6 +58,9 @@ ========== ====================================================================== Version Changes ---------- ---------------------------------------------------------------------- +0.36.2 - Support fastqsanger.gz datatype. If fastqsanger.gz is used as input + the output will also be fastqsanger.gz. + - Use $_JAVA_OPTIONS to customize memory requirements. 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. @@ -82,6 +85,14 @@ ========== ====================================================================== +Credits +======= + +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. + + Developers ========== |
| b |
| diff -r f80107cdc406 -r 141bba0e9a77 test-data/Illumina_SG_R1.fastq.gz |
| b |
| Binary file test-data/Illumina_SG_R1.fastq.gz has changed |
| b |
| diff -r f80107cdc406 -r 141bba0e9a77 test-data/Illumina_SG_R2.fastq.gz |
| b |
| Binary file test-data/Illumina_SG_R2.fastq.gz has changed |
| b |
| diff -r f80107cdc406 -r 141bba0e9a77 test-data/trimmomatic_pe_r1_paired_out1.fastq.gz |
| b |
| Binary file test-data/trimmomatic_pe_r1_paired_out1.fastq.gz has changed |
| b |
| diff -r f80107cdc406 -r 141bba0e9a77 test-data/trimmomatic_pe_r1_unpaired_out1.fastq.gz |
| b |
| Binary file test-data/trimmomatic_pe_r1_unpaired_out1.fastq.gz has changed |
| b |
| diff -r f80107cdc406 -r 141bba0e9a77 test-data/trimmomatic_pe_r2_paired_out1.fastq.gz |
| b |
| Binary file test-data/trimmomatic_pe_r2_paired_out1.fastq.gz has changed |
| b |
| diff -r f80107cdc406 -r 141bba0e9a77 test-data/trimmomatic_pe_r2_unpaired_out1.fastq.gz |
| b |
| Binary file test-data/trimmomatic_pe_r2_unpaired_out1.fastq.gz has changed |
| b |
| diff -r f80107cdc406 -r 141bba0e9a77 test-data/trimmomatic_se_out1.fastq.gz |
| b |
| Binary file test-data/trimmomatic_se_out1.fastq.gz has changed |
| b |
| diff -r f80107cdc406 -r 141bba0e9a77 trimmomatic.xml --- a/trimmomatic.xml Fri Dec 16 11:31:55 2016 -0500 +++ b/trimmomatic.xml Fri Feb 24 05:12:32 2017 -0500 |
| [ |
| b'@@ -1,4 +1,4 @@\n-<tool id="trimmomatic" name="Trimmomatic" version="0.36.1">\n+<tool id="trimmomatic" name="Trimmomatic" version="0.36.2">\n <description>flexible read trimming tool for Illumina NGS data</description>\n <macros>\n <import>trimmomatic_macros.xml</import>\n@@ -6,29 +6,30 @@\n <requirements>\n <requirement type="package" version="0.36">trimmomatic</requirement>\n </requirements>\n- <stdio>\n- <exit_code range="1:" />\n- </stdio>\n- <command><![CDATA[\n+ <command detect_errors="aggressive"><![CDATA[\n @CONDA_TRIMMOMATIC_JAR_PATH@ &&\n @CONDA_TRIMMOMATIC_ADAPTERS_PATH@ &&\n- java -mx8G -jar \\$TRIMMOMATIC_JAR_PATH/trimmomatic.jar\n- #if $paired_end.is_paired_end\n+ #if $readtype.single_or_paired == "pair_of_files"\n+ #set r1_ext = $readtype.fastq_r1_in.extension\n+ #set r2_ext = $readtype.fastq_r2_in.extension\n+ ln -s \'$readtype.fastq_r1_in\' fastq_r1.\'$r1_ext\' &&\n+ ln -s \'$readtype.fastq_r2_in\' fastq_r2.\'$r2_ext\' &&\n+ #elif $readtype.single_or_paired == "collection"\n+ #set r1_ext = $readtype.fastq_pair.forward.extension\n+ #set r2_ext = $readtype.fastq_pair.reverse.extension\n+ ln -s \'$readtype.fastq_pair.forward\' fastq_r1.\'$r1_ext\' &&\n+ ln -s \'$readtype.fastq_pair.reverse\' fastq_r2.\'$r2_ext\' &&\n+ #else\n+ ln -s \'$fastq_in\' fastq_in.\'$fastq_in.extension\' &&\n+ #end if\n+ java \\${_JAVA_OPTIONS:--Xmx8G} -jar \\$TRIMMOMATIC_JAR_PATH/trimmomatic.jar\n+ #if $readtype.single_or_paired in ["pair_of_files","collection"]\n PE -threads \\${GALAXY_SLOTS:-6} -phred33\n- #set $paired_input_type = $paired_end.paired_input_type_conditional.paired_input_type\n- #if $paired_input_type == "pair_of_files"\n- "${paired_end.paired_input_type_conditional.fastq_r1_in}"\n- "${paired_end.paired_input_type_conditional.fastq_r2_in}"\n- "${fastq_out_r1_paired}" "${fastq_out_r1_unpaired}"\n- "${fastq_out_r2_paired}" "${fastq_out_r2_unpaired}"\n- #else\n- "${paired_end.paired_input_type_conditional.fastq_pair.forward}"\n- "${paired_end.paired_input_type_conditional.fastq_pair.reverse}"\n- "${fastq_out_paired.forward}" "${fastq_out_unpaired.forward}"\n- "${fastq_out_paired.reverse}" "${fastq_out_unpaired.reverse}"\n- #end if\n+ fastq_r1.\'$r1_ext\' fastq_r2.\'$r2_ext\'\n+ fastq_out_r1_paired.\'$r1_ext\' fastq_out_r1_unpaired.\'$r1_ext\'\n+ fastq_out_r2_paired.\'$r2_ext\' fastq_out_r2_unpaired.\'$r2_ext\'\n #else\n- SE -threads \\${GALAXY_SLOTS:-6} -phred33 "$fastq_in" "$fastq_out"\n+ SE -threads \\${GALAXY_SLOTS:-6} -phred33 fastq_in.\'$fastq_in.extension\' fastq_out.\'$fastq_in.extension\'\n #end if\n ## ILLUMINACLIP option\n #if $illuminaclip.do_illuminaclip\n@@ -65,148 +66,159 @@\n #end for\n 2>&1 | tee trimmomatic.log &&\n if [ -z "\\$(tail -1 trimmomatic.log | grep "Completed successfully")" ]; then echo "Trimmomatic did not finish successfully" >&2 ; exit 1 ; fi\n+ &&\n+ #if $readtype.single_or_paired == "pair_of_files"\n+ mv fastq_out_r1_paired.\'$r1_ext\' \'${fastq_out_r1_paired}\' &&\n+ mv fastq_out_r1_unpaired.\'$r1_ext\' \'${fastq_out_r1_unpaired}\' &&\n+ mv fastq_out_r2_paired.\'$r2_ext\' \'${fastq_out_r2_paired}\' &&\n+ mv fastq_out_r2_unpaired.\'$r2_ext\' \'${fastq_out_r2_unpaired}\'\n+ #elif $readtype.single_or_paired == "collection"\n+ mv fastq_out_r1_paired.\'$r1_ext\' \'${fastq_out_paired.forward}\' &&\n+ mv fastq_out_r1_unpaired.\'$r1_ext\' \'${fastq_out_unpaired.forward}\' &&\n+ mv fastq_out_r2_paired.\'$r2_ext\' \'${fastq_out_paired.reverse}\' &&\n+ mv fastq_out_r2_unpaired.\'$r2_ext\' \'${fastq_out_unpaired.reverse}\'\n+ #else\n+ mv fastq_out.\'$fastq_in.extension\' \'${fastq_out}\'\n+ #end if\n ]]></command>\n <inputs>\n- <conditional name="paired_end">\n- <param name="is_paired_end" type="boolean" label="Paired end data?" truevalue="yes" falsevalue="no" checked="on" />\n- <when value="no">\n- <param name="fastq_in" type="data" format="fastqsanger" label="Input FASTQ file" />\n+ <conditional name="readtype">\n+ <param name="single_or_paired" '..b' <collection type="paired">\n <element name="forward" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />\n@@ -237,17 +243,36 @@\n </param>\n <param name="operations_0|operation|name" value="SLIDINGWINDOW" />\n <output_collection name="fastq_out_paired" type="paired">\n-\t<element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" />\n-\t<element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" />\n+ <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq" />\n+ <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq" />\n </output_collection>\n <output_collection name="fastq_out_unpaired" type="paired">\n-\t<element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" />\n-\t<element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />\n+ <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq" />\n+ <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq" />\n+ </output_collection>\n+ </test>\n+ <test>\n+ <!-- Paired-end with dataset collection - gzipped -->\n+ <param name="single_or_paired" value="collection" />\n+ <param name="fastq_pair">\n+ <collection type="paired">\n+ <element name="forward" value="Illumina_SG_R1.fastq.gz" ftype="fastqsanger.gz" />\n+ <element name="reverse" value="Illumina_SG_R2.fastq.gz" ftype="fastqsanger.gz"/>\n+ </collection>\n+ </param>\n+ <param name="operations_0|operation|name" value="SLIDINGWINDOW" />\n+ <output_collection name="fastq_out_paired" type="paired">\n+ <element name="forward" file="trimmomatic_pe_r1_paired_out1.fastq.gz" />\n+ <element name="reverse" file="trimmomatic_pe_r2_paired_out1.fastq.gz" />\n+ </output_collection>\n+ <output_collection name="fastq_out_unpaired" type="paired">\n+ <element name="forward" file="trimmomatic_pe_r1_unpaired_out1.fastq.gz" />\n+ <element name="reverse" file="trimmomatic_pe_r2_unpaired_out1.fastq.gz" />\n </output_collection>\n </test>\n <test>\n <!-- Single-end using AVGQUAL -->\n- <param name="is_paired_end" value="no" />\n+ <param name="single_or_paired" value="se" />\n <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />\n <param name="operations_0|operation|name" value="AVGQUAL" />\n <param name="operations_0|operation|avgqual" value="30" />\n@@ -255,7 +280,7 @@\n </test>\n <test>\n <!-- Single-end using MAXINFO -->\n- <param name="is_paired_end" value="no" />\n+ <param name="single_or_paired" value="se" />\n <param name="fastq_in" value="Illumina_SG_R1.fastq" ftype="fastqsanger" />\n <param name="operations_0|operation|name" value="MAXINFO" />\n <param name="operations_0|operation|target_length" value="75" />\n@@ -282,7 +307,7 @@\n * **CROP:** Cut the read to a specified length\n * **HEADCROP:** Cut the specified number of bases from the start of the read\n * **AVGQUAL:** Drop the read if the average quality is below a specified value\n- * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to \n+ * **MAXINFO:** Trim reads adaptively, balancing read length and error rate to\n maximise the value of each read\n \n If ILLUMINACLIP is requested then it is always performed first; subsequent options\n@@ -334,12 +359,15 @@\n **Credits**\n \n This Galaxy tool has been developed within the Bioinformatics Core Facility at the\n-University of Manchester. It runs the Trimmomatic program which has been developed\n+University of Manchester, with contributions from Peter van Heusden and Marius\n+van den Beek.\n+\n+It runs the Trimmomatic program which has been developed\n within Bjorn Usadel\'s group at RWTH Aachen university.\n \n Trimmomatic website (including documentation):\n \n- * http://www.usadellab.org/cms/index.php?page=trimmomatic \n+ * http://www.usadellab.org/cms/index.php?page=trimmomatic\n \n The reference for Trimmomatic is:\n \n' |