Mercurial > repos > bgruening > trim_galore
changeset 18:b94789823aad draft default tip
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f8ccc97b827b98db1bcf42073d3c5eb4e3f134c4
| author | bgruening |
|---|---|
| date | Sat, 10 May 2025 08:09:10 +0000 |
| parents | eefb644655a5 |
| children | |
| files | macros.xml test-data/paired_collection_example_results3.txt test-data/paired_collection_example_results3gz.txt test-data/paired_example_results2.txt test-data/paired_example_results2gz.txt test-data/sanger_full_range_report_results1.txt test-data/sanger_full_range_report_results1gz.txt trim_galore.xml |
| diffstat | 8 files changed, 73 insertions(+), 73 deletions(-) [+] |
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--- a/macros.xml Wed Mar 05 18:50:58 2025 +0000 +++ b/macros.xml Sat May 10 08:09:10 2025 +0000 @@ -1,6 +1,6 @@ <macros> - <token name="@TOOL_VERSION@">0.6.7</token> - <token name="@VERSION_SUFFIX@">1</token> + <token name="@TOOL_VERSION@">0.6.10</token> + <token name="@VERSION_SUFFIX@">0</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">trim-galore</requirement>
--- a/test-data/paired_collection_example_results3.txt Wed Mar 05 18:50:58 2025 +0000 +++ b/test-data/paired_collection_example_results3.txt Sat May 10 08:09:10 2025 +0000 @@ -3,9 +3,9 @@ ========================== Input filename: input_1.fastq Trimming mode: paired-end -Trim Galore version: 0.6.7 -Cutadapt version: 3.4 -Python version: could not detect +Trim Galore version: 0.6.10 +Cutadapt version: 5.0 +Python version: 3.12.10 Number of cores used for trimming: 4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 @@ -18,10 +18,9 @@ Length cut-off for read 2: 35 bp (default) -This is cutadapt 3.4 with Python 3.9.6 +This is cutadapt 5.0 with Python 3.12.10 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq -Processing reads on 4 cores in single-end mode ... -Finished in 0.01 s (115 µs/read; 0.52 M reads/minute). +Processing single-end reads on 4 cores ... === Summary === @@ -37,6 +36,7 @@ Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times +Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1 @@ -87,9 +87,9 @@ ========================== Input filename: input_2.fastq Trimming mode: paired-end -Trim Galore version: 0.6.7 -Cutadapt version: 3.4 -Python version: could not detect +Trim Galore version: 0.6.10 +Cutadapt version: 5.0 +Python version: 3.12.10 Number of cores used for trimming: 4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 @@ -102,10 +102,9 @@ Length cut-off for read 2: 35 bp (default) -This is cutadapt 3.4 with Python 3.9.6 +This is cutadapt 5.0 with Python 3.12.10 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq -Processing reads on 4 cores in single-end mode ... -Finished in 0.02 s (159 µs/read; 0.38 M reads/minute). +Processing single-end reads on 4 cores ... === Summary === @@ -121,6 +120,7 @@ Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times +Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1
--- a/test-data/paired_collection_example_results3gz.txt Wed Mar 05 18:50:58 2025 +0000 +++ b/test-data/paired_collection_example_results3gz.txt Sat May 10 08:09:10 2025 +0000 @@ -3,9 +3,9 @@ ========================== Input filename: input_1.fastq.gz Trimming mode: paired-end -Trim Galore version: 0.6.7 -Cutadapt version: 3.4 -Python version: could not detect +Trim Galore version: 0.6.10 +Cutadapt version: 5.0 +Python version: 3.12.10 Number of cores used for trimming: 4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 @@ -19,10 +19,9 @@ Output file will be GZIP compressed -This is cutadapt 3.4 with Python 3.9.6 +This is cutadapt 5.0 with Python 3.12.10 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz -Processing reads on 4 cores in single-end mode ... -Finished in 0.01 s (129 µs/read; 0.47 M reads/minute). +Processing single-end reads on 4 cores ... === Summary === @@ -38,6 +37,7 @@ Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times +Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1 @@ -88,9 +88,9 @@ ========================== Input filename: input_2.fastq.gz Trimming mode: paired-end -Trim Galore version: 0.6.7 -Cutadapt version: 3.4 -Python version: could not detect +Trim Galore version: 0.6.10 +Cutadapt version: 5.0 +Python version: 3.12.10 Number of cores used for trimming: 4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 @@ -104,10 +104,9 @@ Output file will be GZIP compressed -This is cutadapt 3.4 with Python 3.9.6 +This is cutadapt 5.0 with Python 3.12.10 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz -Processing reads on 4 cores in single-end mode ... -Finished in 0.04 s (395 µs/read; 0.15 M reads/minute). +Processing single-end reads on 4 cores ... === Summary === @@ -123,6 +122,7 @@ Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times +Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1
--- a/test-data/paired_example_results2.txt Wed Mar 05 18:50:58 2025 +0000 +++ b/test-data/paired_example_results2.txt Sat May 10 08:09:10 2025 +0000 @@ -3,9 +3,9 @@ ========================== Input filename: input_1.fastq Trimming mode: paired-end -Trim Galore version: 0.6.7 -Cutadapt version: 3.4 -Python version: could not detect +Trim Galore version: 0.6.10 +Cutadapt version: 5.0 +Python version: 3.12.10 Number of cores used for trimming: 4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 @@ -16,10 +16,9 @@ Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp -This is cutadapt 3.4 with Python 3.9.6 +This is cutadapt 5.0 with Python 3.12.10 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq -Processing reads on 4 cores in single-end mode ... -Finished in 0.01 s (117 µs/read; 0.51 M reads/minute). +Processing single-end reads on 4 cores ... === Summary === @@ -35,6 +34,7 @@ Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times +Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1 @@ -85,9 +85,9 @@ ========================== Input filename: input_2.fastq Trimming mode: paired-end -Trim Galore version: 0.6.7 -Cutadapt version: 3.4 -Python version: could not detect +Trim Galore version: 0.6.10 +Cutadapt version: 5.0 +Python version: 3.12.10 Number of cores used for trimming: 4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 @@ -98,10 +98,9 @@ Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp -This is cutadapt 3.4 with Python 3.9.6 +This is cutadapt 5.0 with Python 3.12.10 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq -Processing reads on 4 cores in single-end mode ... -Finished in 0.03 s (256 µs/read; 0.23 M reads/minute). +Processing single-end reads on 4 cores ... === Summary === @@ -117,6 +116,7 @@ Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times +Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1
--- a/test-data/paired_example_results2gz.txt Wed Mar 05 18:50:58 2025 +0000 +++ b/test-data/paired_example_results2gz.txt Sat May 10 08:09:10 2025 +0000 @@ -3,13 +3,13 @@ ========================== Input filename: input_1.fastq.gz Trimming mode: paired-end -Trim Galore version: 0.6.7 -Cutadapt version: 3.4 -Python version: could not detect +Trim Galore version: 0.6.10 +Cutadapt version: 5.0 +Python version: 3.12.10 Number of cores used for trimming: 4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 -Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0) +Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0) Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp @@ -17,10 +17,9 @@ Output file will be GZIP compressed -This is cutadapt 3.4 with Python 3.9.6 +This is cutadapt 5.0 with Python 3.12.10 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz -Processing reads on 4 cores in single-end mode ... -Finished in 0.01 s (114 µs/read; 0.53 M reads/minute). +Processing single-end reads on 4 cores ... === Summary === @@ -36,6 +35,7 @@ Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times +Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1 @@ -86,13 +86,13 @@ ========================== Input filename: input_2.fastq.gz Trimming mode: paired-end -Trim Galore version: 0.6.7 -Cutadapt version: 3.4 -Python version: could not detect +Trim Galore version: 0.6.10 +Cutadapt version: 5.0 +Python version: 3.12.10 Number of cores used for trimming: 4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 -Using Nextera adapter for trimming (count: 29). Second best hit was Illumina (count: 0) +Using Nextera adapter for trimming (count: 29). Second best hit was smallRNA (count: 0) Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp @@ -100,10 +100,9 @@ Output file will be GZIP compressed -This is cutadapt 3.4 with Python 3.9.6 +This is cutadapt 5.0 with Python 3.12.10 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz -Processing reads on 4 cores in single-end mode ... -Finished in 0.02 s (232 µs/read; 0.26 M reads/minute). +Processing single-end reads on 4 cores ... === Summary === @@ -119,6 +118,7 @@ Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 times +Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-12 bp: 1
--- a/test-data/sanger_full_range_report_results1.txt Wed Mar 05 18:50:58 2025 +0000 +++ b/test-data/sanger_full_range_report_results1.txt Sat May 10 08:09:10 2025 +0000 @@ -3,13 +3,13 @@ ========================== Input filename: input_1.fastq Trimming mode: single-end -Trim Galore version: 0.6.7 -Cutadapt version: 3.4 -Python version: could not detect +Trim Galore version: 0.6.10 +Cutadapt version: 5.0 +Python version: 3.12.10 Number of cores used for trimming: 4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 -Unable to auto-detect most prominent adapter from the first specified file (count Nextera: 0, count smallRNA: 0, count Illumina: 0) +Unable to auto-detect most prominent adapter from the first specified file (count smallRNA: 0, count Nextera: 0, count Illumina: 0) Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior). Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) Maximum trimming error rate: 0.1 (default) @@ -17,10 +17,9 @@ Minimum required sequence length before a sequence gets removed: 20 bp -This is cutadapt 3.4 with Python 3.9.6 +This is cutadapt 5.0 with Python 3.12.10 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq -Processing reads on 4 cores in single-end mode ... -Finished in 0.01 s (5282 µs/read; 0.01 M reads/minute). +Processing single-end reads on 4 cores ... === Summary === @@ -36,6 +35,7 @@ Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times +Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1
--- a/test-data/sanger_full_range_report_results1gz.txt Wed Mar 05 18:50:58 2025 +0000 +++ b/test-data/sanger_full_range_report_results1gz.txt Sat May 10 08:09:10 2025 +0000 @@ -3,13 +3,13 @@ ========================== Input filename: input_1.fastq.gz Trimming mode: single-end -Trim Galore version: 0.6.7 -Cutadapt version: 3.4 -Python version: could not detect +Trim Galore version: 0.6.10 +Cutadapt version: 5.0 +Python version: 3.12.10 Number of cores used for trimming: 4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 -Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count Nextera: 0, count smallRNA: 0) +Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count smallRNA: 0, count Nextera: 0) Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior). Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) Maximum trimming error rate: 0.1 (default) @@ -18,10 +18,9 @@ Output file will be GZIP compressed -This is cutadapt 3.4 with Python 3.9.6 +This is cutadapt 5.0 with Python 3.12.10 Command line parameters: -j 4 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz -Processing reads on 4 cores in single-end mode ... -Finished in 0.01 s (5217 µs/read; 0.01 M reads/minute). +Processing single-end reads on 4 cores ... === Summary === @@ -37,6 +36,7 @@ Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times +Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1
--- a/trim_galore.xml Wed Mar 05 18:50:58 2025 +0000 +++ b/trim_galore.xml Sat May 10 08:09:10 2025 +0000 @@ -415,7 +415,7 @@ <param name="report" value="true" /> </conditional> <output name="trimmed_reads_single" file="sanger_full_range_results1.fastqsanger" ftype="fastqsanger"/> - <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="12" /> + <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="13" /> </test> <test expect_num_outputs="2"> <conditional name="singlePaired"> @@ -427,7 +427,7 @@ <param name="report" value="true" /> </conditional> <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> - <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="12" /> + <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="10" /> </test> <test expect_num_outputs="1"> @@ -486,7 +486,7 @@ </conditional> <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastqsanger" ftype="fastqsanger"/> <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/> - <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" /> + <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="20" /> </test> <test expect_num_outputs="3"> <conditional name="singlePaired"> @@ -500,7 +500,7 @@ </conditional> <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> - <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" /> + <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="20" /> </test> <test expect_num_outputs="7"> @@ -520,7 +520,7 @@ <param name="retain_unpaired_select" value="retain_unpaired_output" /> </conditional> </conditional> - <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="24" /> + <output name="report_file" file="paired_collection_example_results3.txt" ftype="txt" lines_diff="20" /> <output_collection name="trimmed_reads_paired_collection" type="paired"> <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/> <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/> @@ -548,7 +548,7 @@ <param name="retain_unpaired_select" value="retain_unpaired_output" /> </conditional> </conditional> - <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" /> + <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="20" /> <output_collection name="trimmed_reads_paired_collection" type="paired"> <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" decompress="true" /> @@ -811,7 +811,7 @@ | | *option --amplicon* -.. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ +.. _Trim Galore!: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ .. _Multi-tissue DNA methylation age predictor in mouse: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1203-5 ]]></help>