diff test-data/paired_example_results2.txt @ 15:084bbd8ba7b8 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 10a9de2adae04249830c880cf0c55edaa196f3f7

--- a/test-data/paired_example_results2.txt	Thu Jun 01 12:15:10 2017 -0400
+++ b/test-data/paired_example_results2.txt	Tue Jul 30 06:26:49 2019 -0400
@@ -3,8 +3,9 @@
 ==========================
 Input filename: input_1.fastq
 Trimming mode: paired-end
-Trim Galore version: 0.4.3
-Cutadapt version: 1.13
+Trim Galore version: 0.6.3
+Cutadapt version: 2.4
+Number of cores used for trimming: 1
 Quality Phred score cutoff: 20
 Quality encoding type selected: ASCII+33
 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
@@ -13,10 +14,10 @@
 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
 
 
-This is cutadapt 1.13 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 with at most 10.0% errors in single-end mode ...
-Finished in 0.01 s (101 us/read; 0.59 M reads/minute).
+This is cutadapt 2.4 with Python 3.7.3
+Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_1.fastq
+Processing reads on 1 core in single-end mode ...
+Finished in 0.01 s (75 us/read; 0.80 M reads/minute).
 
 === Summary ===
 
@@ -73,7 +74,6 @@
 80	1	0.0	1	1
 86	1	0.0	1	1
 
-
 RUN STATISTICS FOR INPUT FILE: input_1.fastq
 =============================================
 99 sequences processed in total
@@ -83,8 +83,9 @@
 ==========================
 Input filename: input_2.fastq
 Trimming mode: paired-end
-Trim Galore version: 0.4.3
-Cutadapt version: 1.13
+Trim Galore version: 0.6.3
+Cutadapt version: 2.4
+Number of cores used for trimming: 1
 Quality Phred score cutoff: 20
 Quality encoding type selected: ASCII+33
 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
@@ -93,43 +94,43 @@
 Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
 
 
-This is cutadapt 1.13 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 with at most 10.0% errors in single-end mode ...
-Finished in 0.01 s (100 us/read; 0.60 M reads/minute).
+This is cutadapt 2.4 with Python 3.7.3
+Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA input_2.fastq
+Processing reads on 1 core in single-end mode ...
+Finished in 0.00 s (50 us/read; 1.19 M reads/minute).
 
 === Summary ===
 
-Total reads processed:                     100
-Reads with adapters:                        59 (59.0%)
-Reads written (passing filters):           100 (100.0%)
+Total reads processed:                      99
+Reads with adapters:                        58 (58.6%)
+Reads written (passing filters):            99 (100.0%)
 
-Total basepairs processed:        25,100 bp
-Quality-trimmed:                     746 bp (3.0%)
-Total written (filtered):         23,276 bp (92.7%)
+Total basepairs processed:        24,849 bp
+Quality-trimmed:                     745 bp (3.0%)
+Total written (filtered):         23,035 bp (92.7%)
 
 === Adapter 1 ===
 
-Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 59 times.
+Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 58 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%
+  A: 12.1%
+  C: 37.9%
+  G: 8.6%
+  T: 41.4%
   none/other: 0.0%
 
 Overview of removed sequences
 length	count	expect	max.err	error counts
-1	16	25.0	0	16
+1	16	24.8	0	16
 2	7	6.2	0	7
-3	1	1.6	0	1
+3	1	1.5	0	1
 4	2	0.4	0	2
 6	2	0.0	0	2
-9	2	0.0	0	2
+9	1	0.0	0	1
 10	1	0.0	1	1
 13	1	0.0	1	1
 14	2	0.0	1	2
@@ -156,10 +157,9 @@
 67	1	0.0	1	1
 80	1	0.0	1	1
 
-
 RUN STATISTICS FOR INPUT FILE: input_2.fastq
 =============================================
-100 sequences processed in total
+99 sequences processed in total
 
 Total number of sequences analysed for the sequence pair length validation: 99