# HG changeset patch
# User bgruening
# Date 1492694070 14400
# Node ID b4e39d993fc8ce7506fc01d828e1d430c03cf070
# Parent  1bfc7254232e08651537d23cfd183b0596ebb00c
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit bbef69cc08154b5c156c25f9ca43df0915803856

diff -r 1bfc7254232e -r b4e39d993fc8 test-data/bwa-mem-fastq1.fq.gz
Binary file test-data/bwa-mem-fastq1.fq.gz has changed
diff -r 1bfc7254232e -r b4e39d993fc8 test-data/bwa-mem-fastq2.fq.gz
Binary file test-data/bwa-mem-fastq2.fq.gz has changed
diff -r 1bfc7254232e -r b4e39d993fc8 test-data/paired_collection_example_pair1_results3.fastq.gz
Binary file test-data/paired_collection_example_pair1_results3.fastq.gz has changed
diff -r 1bfc7254232e -r b4e39d993fc8 test-data/paired_collection_example_pair2_results3.fastq.gz
Binary file test-data/paired_collection_example_pair2_results3.fastq.gz has changed
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
@@ -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
 
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
@@ -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%)
diff -r 1bfc7254232e -r b4e39d993fc8 test-data/paired_collection_example_unpair1_results3.fastq.gz
Binary file test-data/paired_collection_example_unpair1_results3.fastq.gz has changed
diff -r 1bfc7254232e -r b4e39d993fc8 test-data/paired_collection_example_unpair2_results3.fastq.gz
Binary file test-data/paired_collection_example_unpair2_results3.fastq.gz has changed
diff -r 1bfc7254232e -r b4e39d993fc8 test-data/paired_example_pair1_results2.fastq.gz
Binary file test-data/paired_example_pair1_results2.fastq.gz has changed
diff -r 1bfc7254232e -r b4e39d993fc8 test-data/paired_example_pair2_results2.fastq.gz
Binary file test-data/paired_example_pair2_results2.fastq.gz has changed
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
@@ -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
 
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
@@ -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%)
diff -r 1bfc7254232e -r b4e39d993fc8 test-data/sanger_full_range_original_sanger.fastq.gz
Binary file test-data/sanger_full_range_original_sanger.fastq.gz has changed
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
@@ -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%)
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
@@ -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%)
+
diff -r 1bfc7254232e -r b4e39d993fc8 test-data/sanger_full_range_results1.fastq.gz
Binary file test-data/sanger_full_range_results1.fastq.gz has changed
diff -r 1bfc7254232e -r b4e39d993fc8 test-data/sanger_full_range_results2.fastq.gz
Binary file test-data/sanger_full_range_results2.fastq.gz has changed
diff -r 1bfc7254232e -r b4e39d993fc8 test-data/sanger_full_range_results3.fastq.gz
Binary file test-data/sanger_full_range_results3.fastq.gz has changed
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
@@ -1,4 +1,4 @@
-<tool id="trim_galore" name="Trim Galore!" version="0.4.2">
+<tool id="trim_galore" name="Trim Galore!" version="0.4.3" profile="17.01">
     <!-- Wrapper compatible with Trim Galore! version 0.4 -->
     <description>Quality and adapter trimmer of reads</description>
     <macros>
@@ -49,41 +49,53 @@
         <requirement type="package" version="1.8">cutadapt</requirement>
     </requirements>
     <version_command>
-        perl $__tool_directory__/trim_galore --version
+        perl '$__tool_directory__/trim_galore' --version
     </version_command>
     <command>
 <![CDATA[
 
-        ## trim_galore removes .fastq and .fq file extensions of input files.
-        ## This is essential if Galaxy provides links to files (with real extensions)
-        ## but that behaviour is causing an inconsistency in output filenaming.
-        ## We work around this by linking every file to cwd without file extension
-
+        #set compressed = 'no'
         #if $singlePaired.sPaired == "single":
-            #if str($singlePaired.input_singles).endswith(".gz"):
-                ln -s "${singlePaired.input_singles}" ./input_singles.gz;
+            #if $singlePaired.input_singles.is_of_type("fastq.gz"):
+                #set read1 = 'input_1.fastq.gz'
+                #set compressed = 'gz'
             #else
-                ln -s "${singlePaired.input_singles}" ./input_singles;
+                #set read1 = 'input_1.fastq'
             #end if
+            ln -s '${singlePaired.input_singles}' ${read1} &&
         #elif $singlePaired.sPaired == "paired":
-            #if str($singlePaired.input_mate1).endswith(".gz"):
-                ln -s "${singlePaired.input_mate1}" ./input_mate1.gz;
-                ln -s "${singlePaired.input_mate2}" ./input_mate2.gz;
+            #if $singlePaired.input_mate1.is_of_type("fastq.gz"):
+                #set read1 = 'input_1.fastq.gz'
+                #set compressed = 'gz'
             #else
-                ln -s "${singlePaired.input_mate1}" ./input_mate1;
-                ln -s "${singlePaired.input_mate2}" ./input_mate2;
+                #set read1 = 'input_1.fastq'
             #end if
+            ln -s '${singlePaired.input_mate1}' ${read1} &&
+
+            #if $singlePaired.input_mate2.is_of_type("fastq.gz"):
+                #set read2 = 'input_2.fastq.gz'
+            #else
+                #set read2 = 'input_2.fastq'
+            #end if
+            ln -s '${singlePaired.input_mate2}' ${read2} &&
         #else:
-            #if str($singlePaired.input_mate_pairs.forward).endswith(".gz"):
-                ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1.gz;
-                ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2.gz;
+            #if $singlePaired.input_mate_pairs.forward.is_of_type("fastq.gz"):
+                #set read1 = 'input_1.fastq.gz'
+                #set compressed = 'gz'
             #else
-                ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1;
-                ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2;
+                #set read1 = 'input_1.fastq'
             #end if
+            ln -s '${singlePaired.input_mate_pairs.forward}' ${read1} &&
+
+            #if $singlePaired.input_mate_pairs.reverse.is_of_type("fastq.gz"):
+                #set read2 = 'input_2.fastq.gz'
+            #else
+                #set read2 = 'input_2.fastq'
+            #end if
+            ln -s '${singlePaired.input_mate_pairs.reverse}' ${read2} &&
         #end if
 
-        perl $__tool_directory__/trim_galore
+        perl '$__tool_directory__/trim_galore'
 
         ## we only support fastqsanger
         --phred33
@@ -147,12 +159,7 @@
 
         #if $singlePaired.sPaired == "single":
             ## input sequence
-            #if str($singlePaired.input_singles).endswith(".gz"):
-                ./input_singles.gz
-                --dont_gzip
-            #else
-                ./input_singles
-            #end if
+            ${read1}
         #else:
             --paired
 
@@ -169,39 +176,25 @@
             #end if
 
             ## input sequences
-            #if $singlePaired.sPaired == "paired":
-                #if str($singlePaired.input_mate1).endswith(".gz"):
-                    ./input_mate1.gz
-                    ./input_mate2.gz
-                    --dont_gzip
-                #else
-                    ./input_mate1
-                    ./input_mate2
-                #end if
-            #else:
-                #if str($singlePaired.input_mate_pairs.forward).endswith(".gz"):
-                    ./input_mate1.gz
-                    ./input_mate2.gz
-                    --dont_gzip
-                #else
-                    ./input_mate1
-                    ./input_mate2
-                #end if
-            #end if
+            ${read1}
+            ${read2}
+        #end if
 
+        #if $compressed == 'no':
+            --dont_gzip
         #end if
 
         ##  Trim Galore is finished, rename the output if compressed
         &&
-        if [ -f input_singles.gz_trimmed.fq ] ; then mv input_singles.gz_trimmed.fq input_singles_trimmed.fq ; fi
+        if [ -f input_1_trimmed.fq.gz ] ; then mv input_1_trimmed.fq.gz input_1_trimmed.fq ; fi
         &&
-        if [ -f input_mate1.gz_val_1.fq ] ; then mv input_mate1.gz_val_1.fq input_mate1_val_1.fq ; fi
+        if [ -f input_1_val_1.fq.gz ] ; then mv input_1_val_1.fq.gz input_1_val_1.fq ; fi
         &&
-        if [ -f input_mate2.gz_val_2.fq ] ; then mv input_mate2.gz_val_2.fq input_mate2_val_2.fq ; fi
+        if [ -f input_2_val_2.fq.gz ] ; then mv input_2_val_2.fq.gz input_2_val_2.fq ; fi
         &&
-        if [ -f input_mate1.gz_unpaired_1.fq ] ; then mv input_mate1.gz_unpaired_1.fq input_mate1_unpaired_1.fq ; fi
+        if [ -f input_1_unpaired_1.fq.gz ] ; then mv input_1_unpaired_1.fq.gz input_1_unpaired_1.fq ; fi
         &&
-        if [ -f input_mate2.gz_unpaired_2.fq ] ; then mv input_mate2.gz_unpaired_2.fq input_mate2_unpaired_2.fq ; fi
+        if [ -f input_2_unpaired_2.fq.gz ] ; then mv input_2_unpaired_2.fq.gz input_2_unpaired_2.fq ; fi
 
         ##  Trim Galore! run is finished. Move the report files to the proper place
         #if $params.settingsType == "custom" and $params.report:
@@ -220,7 +213,7 @@
                 <option value="paired_collection">Paired Collection</option>
             </param>
             <when value="single">
-                <param name="input_singles" type="data" format="fastqsanger" label="Reads in FASTQ format" />
+                <param name="input_singles" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
                 <expand macro="adapter_trimming"/>
 
                 <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end">
@@ -230,12 +223,12 @@
                 </param>
             </when>
             <when value="paired">
-                <param name="input_mate1" type="data" format="fastqsanger" label="Reads in FASTQ format" />
-                <param name="input_mate2" type="data" format="fastqsanger" label="Reads in FASTQ format" />
+                <param name="input_mate1" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
+                <param name="input_mate2" type="data" format="fastqsanger,fastqsanger.gz" label="Reads in FASTQ format" />
                 <expand macro="paired_adapter_trimming" />
             </when>
             <when value="paired_collection">
-                <param name="input_mate_pairs" format="fastqsanger" type="data_collection" collection_type="paired"
+                <param name="input_mate_pairs" format="fastqsanger,fastqsanger.gz" type="data_collection" collection_type="paired"
                     label="Select a paired collection" help="See help section for an explanation of dataset collections"/>
                 <expand macro="paired_adapter_trimming" />
             </when>
@@ -293,42 +286,42 @@
 
     </inputs>
     <outputs>
-        <data format="fastqsanger" name="trimmed_reads_single" from_work_dir="input_singles_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
+        <data format_source="input_singles" name="trimmed_reads_single" from_work_dir="input_1_trimmed.fq" label="${tool.name} on ${on_string}: trimmed reads">
             <filter>singlePaired['sPaired'] == "single"</filter>
         </data>
 
         <collection name="trimmed_reads_paired_collection" type="paired" label="${tool.name} on ${on_string}: paired reads">
-            <data name="forward" format="fastqsanger" from_work_dir="input_mate1_val_1.fq" />
-            <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_val_2.fq" />
+            <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_val_1.fq" />
+            <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_val_2.fq" />
             <filter>singlePaired['sPaired'] == "paired_collection"</filter>
         </collection>
 
         <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads">
-            <data name="forward" format="fastqsanger" from_work_dir="input_mate1_unpaired_1.fq" />
-            <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_unpaired_2.fq" />
+            <data name="forward" format_source="input_mate_pairs['forward']" from_work_dir="input_1_unpaired_1.fq" />
+            <data name="reverse" format_source="input_mate_pairs['forward']" from_work_dir="input_2_unpaired_2.fq" />
             <filter>params['settingsType'] == "custom"</filter>
             <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
             <filter>singlePaired['sPaired'] == "paired_collection"</filter>
         </collection>
 
-        <data format="fastqsanger" name="trimmed_reads_pair1" from_work_dir="input_mate1_val_1.fq"
+        <data format_source="input_mate1" name="trimmed_reads_pair1" from_work_dir="input_1_val_1.fq"
             label="${tool.name} on ${on_string}: trimmed reads pair 1">
             <filter>singlePaired['sPaired'] == "paired"</filter>
         </data>
 
-        <data format="fastqsanger" name="trimmed_reads_pair2" from_work_dir="input_mate2_val_2.fq"
+        <data format_source="input_mate2" name="trimmed_reads_pair2" from_work_dir="input_2_val_2.fq"
             label="${tool.name} on ${on_string}: trimmed reads pair 2">
             <filter>singlePaired['sPaired'] == "paired"</filter>
         </data>
 
-        <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_unpaired_1.fq"
+        <data format_source="input_mate1" name="unpaired_reads_1" from_work_dir="input_1_unpaired_1.fq"
             label="${tool.name} on ${on_string}: unpaired reads (1)">
             <filter>params['settingsType'] == "custom"</filter>
             <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
             <filter>singlePaired['sPaired'] == "paired"</filter>
         </data>
 
-        <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_unpaired_2.fq"
+        <data format_source="input_mate2" name="unpaired_reads_2" from_work_dir="input_2_unpaired_2.fq"
             label="${tool.name} on ${on_string}: unpaired reads (2)">
             <filter>params['settingsType'] == "custom"</filter>
             <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter>
@@ -349,6 +342,14 @@
             <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="8" />
         </test>
+        <test>
+            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="sPaired" value="single" />
+            <param name="settingsType" value="custom" />
+            <param name="report" value="true" />
+            <output name="trimmed_reads_single" file="sanger_full_range_results1.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+            <output name="report_file" file="sanger_full_range_report_results1gz.txt" ftype="txt" lines_diff="9" />
+        </test>
 
         <test>
             <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
@@ -356,6 +357,12 @@
             <param name="trimming_select" value="--illumina" />
             <output name="trimmed_reads_single" file="sanger_full_range_results2.fastqsanger" ftype="fastqsanger"/>
         </test>
+        <test>
+            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="sPaired" value="single" />
+            <param name="trimming_select" value="--illumina" />
+            <output name="trimmed_reads_single" file="sanger_full_range_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+        </test>
 
         <test>
             <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" />
@@ -363,6 +370,12 @@
             <param name="adapter" value="AAAGAGC" />
             <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/>
         </test>
+        <test>
+            <param name="input_singles" value="sanger_full_range_original_sanger.fastq.gz" ftype="fastqsanger.gz" />
+            <param name="sPaired" value="single" />
+            <param name="adapter" value="AAAGAGC" />
+            <output name="trimmed_reads_single" file="sanger_full_range_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+        </test>
 
         <test>
             <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" />
@@ -374,6 +387,16 @@
             <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" />
         </test>
+        <test>
+            <param name="input_mate1" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
+            <param name="input_mate2" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
+            <param name="sPaired" value="paired" />
+            <param name="settingsType" value="custom" />
+            <param name="report" value="true" />
+            <output name="trimmed_reads_pair1" file="paired_example_pair1_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+            <output name="trimmed_reads_pair2" file="paired_example_pair2_results2.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+            <output name="report_file" file="paired_example_results2gz.txt" ftype="txt" lines_diff="24" />
+        </test>
 
         <test>
             <param name="input_mate_pairs">
@@ -399,7 +422,31 @@
                 <element name="forward" file="paired_collection_example_unpair1_results3.fastqsanger" ftype="fastqsanger"/>
                 <element name="reverse" file="paired_collection_example_unpair2_results3.fastqsanger" ftype="fastqsanger"/>
             </output_collection>
+        </test>
+        <test>
+            <param name="input_mate_pairs">
+                <collection type="paired">
+                    <element name="forward" value="bwa-mem-fastq1.fq.gz" ftype="fastqsanger.gz" />
+                    <element name="reverse" value="bwa-mem-fastq2.fq.gz" ftype="fastqsanger.gz" />
+                </collection>
+            </param>
 
+            <param name="sPaired" value="paired_collection" />
+            <param name="settingsType" value="custom" />
+            <param name="report" value="true" />
+            <param name="retain_unpaired_select" value="retain_unpaired_output" />
+
+            <output name="report_file" file="paired_collection_example_results3gz.txt" ftype="txt" lines_diff="25" />
+
+            <output_collection name="trimmed_reads_paired_collection" type="paired">
+                <element name="forward" file="paired_collection_example_pair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+                <element name="reverse" file="paired_collection_example_pair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+            </output_collection>
+
+            <output_collection name="trimmed_reads_unpaired_collection" type="paired">
+                <element name="forward" file="paired_collection_example_unpair1_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+                <element name="reverse" file="paired_collection_example_unpair2_results3.fastq.gz" ftype="fastqsanger.gz" compare="sim_size" delta="0"/>
+            </output_collection>
         </test>
     </tests>
     <help>
@@ -443,7 +490,7 @@
 
   * **Illumina small RNA adapters**
 
-      | 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.
+      | 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.
       |
       | *option --small_rna*