| Previous changeset 9:1bfc7254232e (2017-03-16) Next changeset 11:80cd83b11214 (2017-04-24) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856 |
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modified:
test-data/paired_collection_example_results3.txt test-data/paired_example_results2.txt test-data/sanger_full_range_report_results1.txt trim_galore.xml |
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added:
test-data/bwa-mem-fastq1.fq.gz test-data/bwa-mem-fastq2.fq.gz test-data/paired_collection_example_pair1_results3.fastq.gz test-data/paired_collection_example_pair2_results3.fastq.gz test-data/paired_collection_example_results3gz.txt test-data/paired_collection_example_unpair1_results3.fastq.gz test-data/paired_collection_example_unpair2_results3.fastq.gz test-data/paired_example_pair1_results2.fastq.gz test-data/paired_example_pair2_results2.fastq.gz test-data/paired_example_results2gz.txt test-data/sanger_full_range_original_sanger.fastq.gz test-data/sanger_full_range_report_results1gz.txt test-data/sanger_full_range_results1.fastq.gz test-data/sanger_full_range_results2.fastq.gz test-data/sanger_full_range_results3.fastq.gz |
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| diff -r 1bfc7254232e -r b4e39d993fc8 test-data/paired_collection_example_results3.txt --- a/test-data/paired_collection_example_results3.txt Thu Mar 16 13:48:46 2017 -0400 +++ b/test-data/paired_collection_example_results3.txt Thu Apr 20 09:14:30 2017 -0400 |
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| @@ -1,7 +1,7 @@ SUMMARISING RUN PARAMETERS ========================== -Input filename: ./input_mate1 +Input filename: input_1.fastq Trimming mode: paired-end Trim Galore version: 0.4.0 Cutadapt version: 1.8 @@ -15,8 +15,8 @@ Length cut-off for read 2: 35 bp (default) -This is cutadapt 1.8 with Python 2.7.9 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate1 +This is cutadapt 1.8 with Python 3.5.3 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... Finished in 0.10 s (1010 us/read; 0.06 M reads/minute). @@ -76,14 +76,14 @@ 86 1 0.0 1 1 -RUN STATISTICS FOR INPUT FILE: ./input_mate1 +RUN STATISTICS FOR INPUT FILE: input_1.fastq ============================================= 99 sequences processed in total SUMMARISING RUN PARAMETERS ========================== -Input filename: ./input_mate2 +Input filename: input_2.fastq Trimming mode: paired-end Trim Galore version: 0.4.0 Cutadapt version: 1.8 @@ -97,8 +97,8 @@ Length cut-off for read 2: 35 bp (default) -This is cutadapt 1.8 with Python 2.7.9 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate2 +This is cutadapt 1.8 with Python 3.5.3 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... Finished in 0.10 s (1000 us/read; 0.06 M reads/minute). @@ -161,7 +161,7 @@ 80 1 0.0 1 1 -RUN STATISTICS FOR INPUT FILE: ./input_mate2 +RUN STATISTICS FOR INPUT FILE: input_2.fastq ============================================= 100 sequences processed in total |
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| diff -r 1bfc7254232e -r b4e39d993fc8 test-data/paired_collection_example_results3gz.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_collection_example_results3gz.txt Thu Apr 20 09:14:30 2017 -0400 |
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| @@ -0,0 +1,172 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: input_1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Length cut-off for read 1: 35 bp (default) +Length cut-off for read 2: 35 bp (default) +Output file will be GZIP compressed + + +This is cutadapt 1.8 with Python 3.5.3 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (1010 us/read; 0.06 M reads/minute). + +=== Summary === + +Total reads processed: 99 +Reads with adapters: 52 (52.5%) +Reads written (passing filters): 99 (100.0%) + +Total basepairs processed: 24,849 bp +Quality-trimmed: 205 bp (0.8%) +Total written (filtered): 23,339 bp (93.9%) + +=== Adapter 1 === + +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 9.6% + C: 38.5% + G: 23.1% + T: 28.8% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 11 24.8 0 11 +2 5 6.2 0 5 +3 3 1.5 0 3 +4 3 0.4 0 3 +12 1 0.0 1 1 +13 2 0.0 1 2 +14 1 0.0 1 1 +16 1 0.0 1 1 +17 1 0.0 1 0 1 +20 2 0.0 1 2 +21 1 0.0 1 1 +24 1 0.0 1 1 +26 2 0.0 1 2 +31 1 0.0 1 1 +33 1 0.0 1 1 +41 2 0.0 1 2 +49 1 0.0 1 1 +50 1 0.0 1 1 +54 1 0.0 1 1 +56 1 0.0 1 1 +58 2 0.0 1 2 +60 1 0.0 1 1 +67 2 0.0 1 2 +68 1 0.0 1 1 +69 1 0.0 1 1 +73 1 0.0 1 1 +80 1 0.0 1 1 +86 1 0.0 1 1 + + +RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz +============================================= +99 sequences processed in total + + +SUMMARISING RUN PARAMETERS +========================== +Input filename: input_2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Length cut-off for read 1: 35 bp (default) +Length cut-off for read 2: 35 bp (default) +Output file will be GZIP compressed + + +This is cutadapt 1.8 with Python 3.5.3 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (1000 us/read; 0.06 M reads/minute). + +=== Summary === + +Total reads processed: 100 +Reads with adapters: 59 (59.0%) +Reads written (passing filters): 100 (100.0%) + +Total basepairs processed: 25,100 bp +Quality-trimmed: 746 bp (3.0%) +Total written (filtered): 23,276 bp (92.7%) + +=== Adapter 1 === + +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 11.9% + C: 39.0% + G: 8.5% + T: 40.7% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 16 25.0 0 16 +2 7 6.2 0 7 +3 1 1.6 0 1 +4 2 0.4 0 2 +6 2 0.0 0 2 +9 2 0.0 0 2 +10 1 0.0 1 1 +13 1 0.0 1 1 +14 2 0.0 1 2 +15 1 0.0 1 1 +16 1 0.0 1 1 +17 1 0.0 1 1 +19 2 0.0 1 2 +21 1 0.0 1 1 +25 1 0.0 1 1 +30 1 0.0 1 1 +32 2 0.0 1 2 +34 1 0.0 1 1 +36 2 0.0 1 2 +38 1 0.0 1 1 +40 1 0.0 1 1 +41 1 0.0 1 1 +42 1 0.0 1 1 +43 1 0.0 1 1 +49 1 0.0 1 1 +51 1 0.0 1 1 +56 1 0.0 1 1 +57 1 0.0 1 1 +60 1 0.0 1 1 +67 1 0.0 1 1 +80 1 0.0 1 1 + + +RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz +============================================= +100 sequences processed in total + +Total number of sequences analysed for the sequence pair length validation: 99 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%) |
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| diff -r 1bfc7254232e -r b4e39d993fc8 test-data/paired_example_results2.txt --- a/test-data/paired_example_results2.txt Thu Mar 16 13:48:46 2017 -0400 +++ b/test-data/paired_example_results2.txt Thu Apr 20 09:14:30 2017 -0400 |
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| @@ -1,7 +1,7 @@ SUMMARISING RUN PARAMETERS ========================== -Input filename: ./input_mate1 +Input filename: input_1.fastq Trimming mode: paired-end Trim Galore version: 0.4.0 Cutadapt version: 1.8 @@ -13,8 +13,8 @@ Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp -This is cutadapt 1.8 with Python 2.7.9 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate1 +This is cutadapt 1.8 with Python 3.5.3 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... Finished in 0.10 s (1010 us/read; 0.06 M reads/minute). @@ -74,14 +74,14 @@ 86 1 0.0 1 1 -RUN STATISTICS FOR INPUT FILE: ./input_mate1 +RUN STATISTICS FOR INPUT FILE: input_1.fastq ============================================= 99 sequences processed in total SUMMARISING RUN PARAMETERS ========================== -Input filename: ./input_mate2 +Input filename: input_2.fastq Trimming mode: paired-end Trim Galore version: 0.4.0 Cutadapt version: 1.8 @@ -93,8 +93,8 @@ Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp -This is cutadapt 1.8 with Python 2.7.9 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA ./input_mate2 +This is cutadapt 1.8 with Python 3.5.3 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... Finished in 0.10 s (1000 us/read; 0.06 M reads/minute). @@ -157,7 +157,7 @@ 80 1 0.0 1 1 -RUN STATISTICS FOR INPUT FILE: ./input_mate2 +RUN STATISTICS FOR INPUT FILE: input_2.fastq ============================================= 100 sequences processed in total |
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| diff -r 1bfc7254232e -r b4e39d993fc8 test-data/paired_example_results2gz.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/paired_example_results2gz.txt Thu Apr 20 09:14:30 2017 -0400 |
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| @@ -0,0 +1,168 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: input_1.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Output file will be GZIP compressed + + +This is cutadapt 1.8 with Python 3.5.3 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq.gz +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (1010 us/read; 0.06 M reads/minute). + +=== Summary === + +Total reads processed: 99 +Reads with adapters: 52 (52.5%) +Reads written (passing filters): 99 (100.0%) + +Total basepairs processed: 24,849 bp +Quality-trimmed: 205 bp (0.8%) +Total written (filtered): 23,339 bp (93.9%) + +=== Adapter 1 === + +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 52 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 9.6% + C: 38.5% + G: 23.1% + T: 28.8% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 11 24.8 0 11 +2 5 6.2 0 5 +3 3 1.5 0 3 +4 3 0.4 0 3 +12 1 0.0 1 1 +13 2 0.0 1 2 +14 1 0.0 1 1 +16 1 0.0 1 1 +17 1 0.0 1 0 1 +20 2 0.0 1 2 +21 1 0.0 1 1 +24 1 0.0 1 1 +26 2 0.0 1 2 +31 1 0.0 1 1 +33 1 0.0 1 1 +41 2 0.0 1 2 +49 1 0.0 1 1 +50 1 0.0 1 1 +54 1 0.0 1 1 +56 1 0.0 1 1 +58 2 0.0 1 2 +60 1 0.0 1 1 +67 2 0.0 1 2 +68 1 0.0 1 1 +69 1 0.0 1 1 +73 1 0.0 1 1 +80 1 0.0 1 1 +86 1 0.0 1 1 + + +RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz +============================================= +99 sequences processed in total + + +SUMMARISING RUN PARAMETERS +========================== +Input filename: input_2.fastq.gz +Trimming mode: paired-end +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp +Output file will be GZIP compressed + + +This is cutadapt 1.8 with Python 3.5.3 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq.gz +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (1000 us/read; 0.06 M reads/minute). + +=== Summary === + +Total reads processed: 100 +Reads with adapters: 59 (59.0%) +Reads written (passing filters): 100 (100.0%) + +Total basepairs processed: 25,100 bp +Quality-trimmed: 746 bp (3.0%) +Total written (filtered): 23,276 bp (92.7%) + +=== Adapter 1 === + +Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times. + +No. of allowed errors: +0-9 bp: 0; 10-12 bp: 1 + +Bases preceding removed adapters: + A: 11.9% + C: 39.0% + G: 8.5% + T: 40.7% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 16 25.0 0 16 +2 7 6.2 0 7 +3 1 1.6 0 1 +4 2 0.4 0 2 +6 2 0.0 0 2 +9 2 0.0 0 2 +10 1 0.0 1 1 +13 1 0.0 1 1 +14 2 0.0 1 2 +15 1 0.0 1 1 +16 1 0.0 1 1 +17 1 0.0 1 1 +19 2 0.0 1 2 +21 1 0.0 1 1 +25 1 0.0 1 1 +30 1 0.0 1 1 +32 2 0.0 1 2 +34 1 0.0 1 1 +36 2 0.0 1 2 +38 1 0.0 1 1 +40 1 0.0 1 1 +41 1 0.0 1 1 +42 1 0.0 1 1 +43 1 0.0 1 1 +49 1 0.0 1 1 +51 1 0.0 1 1 +56 1 0.0 1 1 +57 1 0.0 1 1 +60 1 0.0 1 1 +67 1 0.0 1 1 +80 1 0.0 1 1 + + +RUN STATISTICS FOR INPUT FILE: input_2.fastq.gz +============================================= +100 sequences processed in total + +Total number of sequences analysed for the sequence pair length validation: 99 + +Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1 (1.01%) |
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| diff -r 1bfc7254232e -r b4e39d993fc8 test-data/sanger_full_range_report_results1.txt --- a/test-data/sanger_full_range_report_results1.txt Thu Mar 16 13:48:46 2017 -0400 +++ b/test-data/sanger_full_range_report_results1.txt Thu Apr 20 09:14:30 2017 -0400 |
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| @@ -1,7 +1,7 @@ SUMMARISING RUN PARAMETERS ========================== -Input filename: ./input_singles +Input filename: input_1.fastq Trimming mode: single-end Trim Galore version: 0.4.0 Cutadapt version: 1.8 @@ -13,8 +13,8 @@ Minimum required sequence length before a sequence gets removed: 20 bp -This is cutadapt 1.8 with Python 2.7.9 -Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ./input_singles +This is cutadapt 1.8 with Python 3.5.3 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... Finished in 0.10 s (50000 us/read; 0.00 M reads/minute). @@ -47,7 +47,7 @@ 1 1 0.5 0 1 -RUN STATISTICS FOR INPUT FILE: ./input_singles +RUN STATISTICS FOR INPUT FILE: input_1.fastq ============================================= 2 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 0 (0.0%) |
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| diff -r 1bfc7254232e -r b4e39d993fc8 test-data/sanger_full_range_report_results1gz.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/sanger_full_range_report_results1gz.txt Thu Apr 20 09:14:30 2017 -0400 |
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| @@ -0,0 +1,55 @@ + +SUMMARISING RUN PARAMETERS +========================== +Input filename: input_1.fastq.gz +Trimming mode: single-end +Trim Galore version: 0.4.0 +Cutadapt version: 1.8 +Quality Phred score cutoff: 20 +Quality encoding type selected: ASCII+33 +Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) +Maximum trimming error rate: 0.1 (default) +Minimum required adapter overlap (stringency): 1 bp +Minimum required sequence length before a sequence gets removed: 20 bp +Output file will be GZIP compressed + + +This is cutadapt 1.8 with Python 3.5.3 +Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC input_1.fastq.gz +Trimming 1 adapter(s) with at most 10.0% errors in single-end mode ... +Finished in 0.10 s (50000 us/read; 0.00 M reads/minute). + +=== Summary === + +Total reads processed: 2 +Reads with adapters: 1 (50.0%) +Reads written (passing filters): 2 (100.0%) + +Total basepairs processed: 188 bp +Quality-trimmed: 20 bp (10.6%) +Total written (filtered): 167 bp (88.8%) + +=== Adapter 1 === + +Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1 times. + +No. of allowed errors: +0-9 bp: 0; 10-13 bp: 1 + +Bases preceding removed adapters: + A: 0.0% + C: 100.0% + G: 0.0% + T: 0.0% + none/other: 0.0% + +Overview of removed sequences +length count expect max.err error counts +1 1 0.5 0 1 + + +RUN STATISTICS FOR INPUT FILE: input_1.fastq.gz +============================================= +2 sequences processed in total +Sequences removed because they became shorter than the length cutoff of 20 bp: 0 (0.0%) + |
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| diff -r 1bfc7254232e -r b4e39d993fc8 trim_galore.xml --- a/trim_galore.xml Thu Mar 16 13:48:46 2017 -0400 +++ b/trim_galore.xml Thu Apr 20 09:14:30 2017 -0400 |
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| b'@@ -1,4 +1,4 @@\n-<tool id="trim_galore" name="Trim Galore!" version="0.4.2">\n+<tool id="trim_galore" name="Trim Galore!" version="0.4.3" profile="17.01">\n <!-- Wrapper compatible with Trim Galore! version 0.4 -->\n <description>Quality and adapter trimmer of reads</description>\n <macros>\n@@ -49,41 +49,53 @@\n <requirement type="package" version="1.8">cutadapt</requirement>\n </requirements>\n <version_command>\n- perl $__tool_directory__/trim_galore --version\n+ perl \'$__tool_directory__/trim_galore\' --version\n </version_command>\n <command>\n <![CDATA[\n \n- ## trim_galore removes .fastq and .fq file extensions of input files.\n- ## This is essential if Galaxy provides links to files (with real extensions)\n- ## but that behaviour is causing an inconsistency in output filenaming.\n- ## We work around this by linking every file to cwd without file extension\n-\n+ #set compressed = \'no\'\n #if $singlePaired.sPaired == "single":\n- #if str($singlePaired.input_singles).endswith(".gz"):\n- ln -s "${singlePaired.input_singles}" ./input_singles.gz;\n+ #if $singlePaired.input_singles.is_of_type("fastq.gz"):\n+ #set read1 = \'input_1.fastq.gz\'\n+ #set compressed = \'gz\'\n #else\n- ln -s "${singlePaired.input_singles}" ./input_singles;\n+ #set read1 = \'input_1.fastq\'\n #end if\n+ ln -s \'${singlePaired.input_singles}\' ${read1} &&\n #elif $singlePaired.sPaired == "paired":\n- #if str($singlePaired.input_mate1).endswith(".gz"):\n- ln -s "${singlePaired.input_mate1}" ./input_mate1.gz;\n- ln -s "${singlePaired.input_mate2}" ./input_mate2.gz;\n+ #if $singlePaired.input_mate1.is_of_type("fastq.gz"):\n+ #set read1 = \'input_1.fastq.gz\'\n+ #set compressed = \'gz\'\n #else\n- ln -s "${singlePaired.input_mate1}" ./input_mate1;\n- ln -s "${singlePaired.input_mate2}" ./input_mate2;\n+ #set read1 = \'input_1.fastq\'\n #end if\n+ ln -s \'${singlePaired.input_mate1}\' ${read1} &&\n+\n+ #if $singlePaired.input_mate2.is_of_type("fastq.gz"):\n+ #set read2 = \'input_2.fastq.gz\'\n+ #else\n+ #set read2 = \'input_2.fastq\'\n+ #end if\n+ ln -s \'${singlePaired.input_mate2}\' ${read2} &&\n #else:\n- #if str($singlePaired.input_mate_pairs.forward).endswith(".gz"):\n- ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1.gz;\n- ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2.gz;\n+ #if $singlePaired.input_mate_pairs.forward.is_of_type("fastq.gz"):\n+ #set read1 = \'input_1.fastq.gz\'\n+ #set compressed = \'gz\'\n #else\n- ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1;\n- ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2;\n+ #set read1 = \'input_1.fastq\'\n #end if\n+ ln -s \'${singlePaired.input_mate_pairs.forward}\' ${read1} &&\n+\n+ #if $singlePaired.input_mate_pairs.reverse.is_of_type("fastq.gz"):\n+ #set read2 = \'input_2.fastq.gz\'\n+ #else\n+ #set read2 = \'input_2.fastq\'\n+ #end if\n+ ln -s \'${singlePaired.input_mate_pairs.reverse}\' ${read2} &&\n #end if\n \n- perl $__tool_directory__/trim_galore\n+ perl \'$__tool_directory__/trim_galore\'\n \n ## we only support fastqsanger\n --phred33\n@@ -147,12 +159,7 @@\n \n #if $singlePaired.sPaired == "single":\n ## input sequence\n- #if str($singlePaired.input_singles).endswith(".gz"):\n- ./input_singles.gz\n- --dont_gzip\n- #else\n- ./input_sing'..b'@\n <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastqsanger" ftype="fastqsanger"/>\n <output name="report_file" file="paired_example_results2.txt" ftype="txt" lines_diff="24" />\n </test>\n+ <test>\n+ <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />\n+ <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />\n+ <param name="sPaired" value="paired" />\n+ <param name="settingsType" value="custom" />\n+ <param name="report" value="true" />\n+ <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>\n+ <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>\n+ <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />\n+ </test>\n \n <test>\n <param name="input_mate_pairs">\n@@ -399,7 +422,31 @@\n <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>\n <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>\n </output_collection>\n+ </test>\n+ <test>\n+ <param name="input_mate_pairs">\n+ <collection type="paired">\n+ <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />\n+ <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />\n+ </collection>\n+ </param>\n \n+ <param name="sPaired" value="paired_collection" />\n+ <param name="settingsType" value="custom" />\n+ <param name="report" value="true" />\n+ <param name="retain_unpaired_select" value="retain_unpaired_output" />\n+\n+ <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />\n+\n+ <output_collection name="trimmed_reads_paired_collection" type="paired">\n+ <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>\n+ <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>\n+ </output_collection>\n+\n+ <output_collection name="trimmed_reads_unpaired_collection" type="paired">\n+ <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>\n+ <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>\n+ </output_collection>\n </test>\n </tests>\n <help>\n@@ -443,7 +490,7 @@\n \n * **Illumina small RNA adapters**\n \n- | Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA 3\' Adapter \'TGGAATTCTCGG\' instead of the default auto-detection of adapter sequence. Selecting to trim smallRNA adapters will also lower the --length value to 18bp. If the smallRNA libraries are paired-end then -a2 will be set to the Illumina small RNA 5\' adapter automatically (\xe2\x80\x98GATCGTCGGACT\xe2\x80\x99) unless -a 2 had been defined explicitly.\n+ | Adapter sequence to be trimmed is the first 12bp of the Illumina Small RNA 3\' Adapter \'TGGAATTCTCGG\' instead of the default auto-detection of adapter sequence. Selecting to trim smallRNA adapters will also lower the --length value to 18bp. If the smallRNA libraries are paired-end then -a2 will be set to the Illumina small RNA 5\' adapter automatically (\'GATCGTCGGACT\') unless -a 2 had been defined explicitly.\n |\n | *option --small_rna*\n \n' |