| Previous changeset 10:b4e39d993fc8 (2017-04-20) Next changeset 12:1bf4789584dc (2017-05-16) |
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Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 78bee2b2efd36fe9399ce574159fc007cb6bdfbf |
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modified:
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 |
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removed:
tool_dependencies.xml trim_galore |
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| diff -r b4e39d993fc8 -r 80cd83b11214 test-data/paired_collection_example_results3.txt --- a/test-data/paired_collection_example_results3.txt Thu Apr 20 09:14:30 2017 -0400 +++ b/test-data/paired_collection_example_results3.txt Mon Apr 24 14:30:07 2017 -0400 |
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| @@ -3,8 +3,8 @@ ========================== Input filename: input_1.fastq Trimming mode: paired-end -Trim Galore version: 0.4.0 -Cutadapt version: 1.8 +Trim Galore version: 0.4.3 +Cutadapt version: 1.13 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) @@ -15,10 +15,10 @@ Length cut-off for read 2: 35 bp (default) -This is cutadapt 1.8 with Python 3.5.3 +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(s) with at most 10.0% errors in single-end mode ... -Finished in 0.10 s (1010 us/read; 0.06 M reads/minute). +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). === Summary === @@ -85,8 +85,8 @@ ========================== Input filename: input_2.fastq Trimming mode: paired-end -Trim Galore version: 0.4.0 -Cutadapt version: 1.8 +Trim Galore version: 0.4.3 +Cutadapt version: 1.13 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) @@ -97,10 +97,10 @@ Length cut-off for read 2: 35 bp (default) -This is cutadapt 1.8 with Python 3.5.3 +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(s) with at most 10.0% errors in single-end mode ... -Finished in 0.10 s (1000 us/read; 0.06 M reads/minute). +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). === Summary === |
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| diff -r b4e39d993fc8 -r 80cd83b11214 test-data/paired_collection_example_results3gz.txt --- a/test-data/paired_collection_example_results3gz.txt Thu Apr 20 09:14:30 2017 -0400 +++ b/test-data/paired_collection_example_results3gz.txt Mon Apr 24 14:30:07 2017 -0400 |
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| @@ -3,8 +3,8 @@ ========================== Input filename: input_1.fastq.gz Trimming mode: paired-end -Trim Galore version: 0.4.0 -Cutadapt version: 1.8 +Trim Galore version: 0.4.3 +Cutadapt version: 1.13 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) @@ -16,10 +16,10 @@ Output file will be GZIP compressed -This is cutadapt 1.8 with Python 3.5.3 +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.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). +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). === Summary === @@ -86,8 +86,8 @@ ========================== Input filename: input_2.fastq.gz Trimming mode: paired-end -Trim Galore version: 0.4.0 -Cutadapt version: 1.8 +Trim Galore version: 0.4.3 +Cutadapt version: 1.13 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) @@ -99,10 +99,10 @@ Output file will be GZIP compressed -This is cutadapt 1.8 with Python 3.5.3 +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.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). +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). === Summary === |
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| diff -r b4e39d993fc8 -r 80cd83b11214 test-data/paired_example_results2.txt --- a/test-data/paired_example_results2.txt Thu Apr 20 09:14:30 2017 -0400 +++ b/test-data/paired_example_results2.txt Mon Apr 24 14:30:07 2017 -0400 |
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| @@ -3,8 +3,8 @@ ========================== Input filename: input_1.fastq Trimming mode: paired-end -Trim Galore version: 0.4.0 -Cutadapt version: 1.8 +Trim Galore version: 0.4.3 +Cutadapt version: 1.13 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) @@ -13,10 +13,10 @@ Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp -This is cutadapt 1.8 with Python 3.5.3 +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(s) with at most 10.0% errors in single-end mode ... -Finished in 0.10 s (1010 us/read; 0.06 M reads/minute). +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). === Summary === @@ -83,8 +83,8 @@ ========================== Input filename: input_2.fastq Trimming mode: paired-end -Trim Galore version: 0.4.0 -Cutadapt version: 1.8 +Trim Galore version: 0.4.3 +Cutadapt version: 1.13 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) @@ -93,10 +93,10 @@ Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp -This is cutadapt 1.8 with Python 3.5.3 +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(s) with at most 10.0% errors in single-end mode ... -Finished in 0.10 s (1000 us/read; 0.06 M reads/minute). +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). === Summary === |
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| diff -r b4e39d993fc8 -r 80cd83b11214 test-data/paired_example_results2gz.txt --- a/test-data/paired_example_results2gz.txt Thu Apr 20 09:14:30 2017 -0400 +++ b/test-data/paired_example_results2gz.txt Mon Apr 24 14:30:07 2017 -0400 |
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| @@ -3,8 +3,8 @@ ========================== Input filename: input_1.fastq.gz Trimming mode: paired-end -Trim Galore version: 0.4.0 -Cutadapt version: 1.8 +Trim Galore version: 0.4.3 +Cutadapt version: 1.13 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) @@ -14,10 +14,10 @@ Output file will be GZIP compressed -This is cutadapt 1.8 with Python 3.5.3 +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.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). +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). === Summary === @@ -84,8 +84,8 @@ ========================== Input filename: input_2.fastq.gz Trimming mode: paired-end -Trim Galore version: 0.4.0 -Cutadapt version: 1.8 +Trim Galore version: 0.4.3 +Cutadapt version: 1.13 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) @@ -95,10 +95,10 @@ Output file will be GZIP compressed -This is cutadapt 1.8 with Python 3.5.3 +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.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). +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). === Summary === |
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| diff -r b4e39d993fc8 -r 80cd83b11214 test-data/sanger_full_range_report_results1.txt --- a/test-data/sanger_full_range_report_results1.txt Thu Apr 20 09:14:30 2017 -0400 +++ b/test-data/sanger_full_range_report_results1.txt Mon Apr 24 14:30:07 2017 -0400 |
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| @@ -3,8 +3,8 @@ ========================== Input filename: input_1.fastq Trimming mode: single-end -Trim Galore version: 0.4.0 -Cutadapt version: 1.8 +Trim Galore version: 0.4.3 +Cutadapt version: 1.13 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) @@ -13,10 +13,10 @@ Minimum required sequence length before a sequence gets removed: 20 bp -This is cutadapt 1.8 with Python 3.5.3 +This is cutadapt 1.13 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). +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 0.01 s (5000 us/read; 0.01 M reads/minute). === Summary === |
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| diff -r b4e39d993fc8 -r 80cd83b11214 test-data/sanger_full_range_report_results1gz.txt --- a/test-data/sanger_full_range_report_results1gz.txt Thu Apr 20 09:14:30 2017 -0400 +++ b/test-data/sanger_full_range_report_results1gz.txt Mon Apr 24 14:30:07 2017 -0400 |
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| @@ -3,8 +3,8 @@ ========================== Input filename: input_1.fastq.gz Trimming mode: single-end -Trim Galore version: 0.4.0 -Cutadapt version: 1.8 +Trim Galore version: 0.4.3 +Cutadapt version: 1.13 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) @@ -14,10 +14,10 @@ Output file will be GZIP compressed -This is cutadapt 1.8 with Python 3.5.3 +This is cutadapt 1.13 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). +Trimming 1 adapter with at most 10.0% errors in single-end mode ... +Finished in 0.01 s (5000 us/read; 0.01 M reads/minute). === Summary === |
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| diff -r b4e39d993fc8 -r 80cd83b11214 tool_dependencies.xml --- a/tool_dependencies.xml Thu Apr 20 09:14:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,6 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="cutadapt" version="1.8"> - <repository changeset_revision="980a47047f57" name="package_cutadapt_1_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" /> - </package> -</tool_dependency> |
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| diff -r b4e39d993fc8 -r 80cd83b11214 trim_galore --- a/trim_galore Thu Apr 20 09:14:30 2017 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| b'@@ -1,1609 +0,0 @@\n-#!/usr/bin/perl\n-use strict;\n-use warnings;\n-use Getopt::Long;\n-use IPC::Open3;\n-use File::Spec;\n-use File::Basename;\n-use Cwd;\n-\n-## This program is Copyright (C) 2012-14, Felix Krueger (felix.krueger@babraham.ac.uk)\n-\n-## This program is free software: you can redistribute it and/or modify\n-## it under the terms of the GNU General Public License as published by\n-## the Free Software Foundation, either version 3 of the License, or\n-## (at your option) any later version.\n-\n-## This program is distributed in the hope that it will be useful,\n-## but WITHOUT ANY WARRANTY; without even the implied warranty of\n-## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\n-## GNU General Public License for more details.\n-\n-## You should have received a copy of the GNU General Public License\n-## along with this program. If not, see <http://www.gnu.org/licenses/>.\n-\n-\n-## this script is taking in FastQ sequences and trims them using Cutadapt\n-\n-## last modified on 01 May 2015\n-\n-my $DOWARN = 1; # print on screen warning and text by default\n-BEGIN { $SIG{\'__WARN__\'} = sub { warn $_[0] if $DOWARN } };\n-\n-my $trimmer_version = \'0.4.0\';\n-\n-\n-my ($cutoff,$adapter,$stringency,$rrbs,$length_cutoff,$keep,$fastqc,$non_directional,$phred_encoding,$fastqc_args,$trim,$gzip,$validate,$retain,$length_read_1,$length_read_2,$a2,$error_rate,$output_dir,$no_report_file,$dont_gzip,$clip_r1,$clip_r2,$three_prime_clip_r1,$three_prime_clip_r2,$nextera,$small_rna,$path_to_cutadapt,$illumina) = process_commandline();\n-\n-my @filenames = @ARGV;\n-die "\\nPlease provide the filename(s) of one or more FastQ file(s) to launch Trim Galore!\\n\n-USAGE: \'trim_galore [options] <filename(s)>\' or \'trim_galore --help\' for more options\\n\\n" unless (@filenames);\n-file_sanity_check($filenames[0]);\n-\n-\n-########################################################################\n-\n-my $path_to_fastqc = \'fastqc\';\n-\n-# Before we start let\'s have quick look if Cutadapt seems to be working with the path information provided\n-# To change the path to Cutadapt use --path_to_cutadapt /full/path/to/the/Cutadapt/executable\n-\n-if(defined $path_to_cutadapt){\n- warn "Path to Cutadapt set as: \'$path_to_cutadapt\' (user defined)\\n";\n- # we\'ll simply use this\n-}\n-else{\n- $path_to_cutadapt = \'cutadapt\'; # default, assuming it is in the PATH\n- warn "Path to Cutadapt set as: \'$path_to_cutadapt\' (default)\\n";\n-}\n-my $cutadapt_version;\n-my $return = system "$path_to_cutadapt --version"; #>/dev/null 2>&1";\n-if ($return == -1){\n- die "Failed to execute Cutadapt porperly. Please install Cutadapt first and make sure it is in the PATH, or specify the path to the Cutadapt executable using --path_to_cutadapt /path/to/cutadapt\\n\\n";\n-}\n-else{\n- warn "Cutadapt seems to be working fine (tested command \'$path_to_cutadapt --version\')\\n";\n- $cutadapt_version = `$path_to_cutadapt --version`;\n- chomp $cutadapt_version;\n- # warn "Cutadapt version: $cutadapt_version\\n";\n-}\n-\n-\n-########################################################################\n-\n-sub autodetect_adapter_type{\n- warn "\\n\\nAUTO-DETECTING ADAPTER TYPE\\n===========================\\n";\n- warn "Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> $ARGV[0] <<)\\n\\n";\n-\n- if ($ARGV[0] =~ /gz$/){\n- open (AUTODETECT,"zcat $ARGV[0] |") or die "Failed to read from file $ARGV[0]\\n";\n- }\n- else{\n- open (AUTODETECT,$ARGV[0]) or die "Failed to read from file $ARGV[0]\\n";\n- }\n-\n- my %adapters;\n-\n- $adapters{\'Illumina\'} -> {seq} = \'AGATCGGAAGAGC\';\n- $adapters{\'Illumina\'} -> {count}= 0;\n- $adapters{\'Illumina\'} -> {name}= \'Illumina TruSeq, Sanger iPCR; auto-detected\';\n-\n- $adapters{\'Nextera\'} -> {seq} = \'CTGTCTCTTATA\';\n- $adapters{\'Nextera\'} -> {count}= 0;\n- $adapters{\'Nextera\'} -> {name}= \'Nextera Transposase sequence; auto-detected\';\n-\n- $adapters{\'smallRNA\'} -> {seq} = \'ATGGAATTCTCG\';\n- $adapters{\'smallRNA\'} -> {count}= 0;\n- $adapters{\'smallRNA\'} -> {na'..b"he\n- second MspI site in a sequence is used for methylation calls. Sequences which\n- were merely trimmed because of poor quality will not be shortened further.\n-\n---non_directional Selecting this option for non-directional RRBS libraries will screen\n- quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read\n- and, if found, removes the first two basepairs. Like with the option\n- '--rrbs' this avoids using cytosine positions that were filled-in\n- during the end-repair step. '--non_directional' requires '--rrbs' to\n- be specified as well.\n-\n---keep Keep the quality trimmed intermediate file. Default: off, which means\n- the temporary file is being deleted after adapter trimming. Only has\n- an effect for RRBS samples since other FastQ files are not trimmed\n- for poor qualities separately.\n-\n-\n-Note for RRBS using MseI:\n-\n-If your DNA material was digested with MseI (recognition motif: TTAA) instead of MspI it is NOT necessary\n-to specify --rrbs or --non_directional since virtually all reads should start with the sequence\n-'TAA', and this holds true for both directional and non-directional libraries. As the end-repair of 'TAA'\n-restricted sites does not involve any cytosines it does not need to be treated especially. Instead, simply\n-run Trim Galore! in the standard (i.e. non-RRBS) mode.\n-\n-\n-Paired-end specific options:\n-\n---paired This option performs length trimming of quality/adapter/RRBS trimmed reads for\n- paired-end files. To pass the validation test, both sequences of a sequence pair\n- are required to have a certain minimum length which is governed by the option\n- --length (see above). If only one read passes this length threshold the\n- other read can be rescued (see option --retain_unpaired). Using this option lets\n- you discard too short read pairs without disturbing the sequence-by-sequence order\n- of FastQ files which is required by many aligners.\n-\n- Trim Galore! expects paired-end files to be supplied in a pairwise fashion, e.g.\n- file1_1.fq file1_2.fq SRR2_1.fq.gz SRR2_2.fq.gz ... .\n-\n--t/--trim1 Trims 1 bp off every read from its 3' end. This may be needed for FastQ files that\n- are to be aligned as paired-end data with Bowtie. This is because Bowtie (1) regards\n- alignments like this:\n-\n- R1 ---------------------------> or this: -----------------------> R1\n- R2 <--------------------------- <----------------- R2\n-\n- as invalid (whenever a start/end coordinate is contained within the other read).\n-\n---retain_unpaired If only one of the two paired-end reads became too short, the longer\n- read will be written to either '.unpaired_1.fq' or '.unpaired_2.fq'\n- output files. The length cutoff for unpaired single-end reads is\n- governed by the parameters -r1/--length_1 and -r2/--length_2. Default: OFF.\n-\n--r1/--length_1 <INT> Unpaired single-end read length cutoff needed for read 1 to be written to\n- '.unpaired_1.fq' output file. These reads may be mapped in single-end mode.\n- Default: 35 bp.\n-\n--r2/--length_2 <INT> Unpaired single-end read length cutoff needed for read 2 to be written to\n- '.unpaired_2.fq' output file. These reads may be mapped in single-end mode.\n- Default: 35 bp.\n-\n-\n-Last modified on 06 May 2015.\n-\n-HELP\n- exit;\n-}\n" |
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| diff -r b4e39d993fc8 -r 80cd83b11214 trim_galore.xml --- a/trim_galore.xml Thu Apr 20 09:14:30 2017 -0400 +++ b/trim_galore.xml Mon Apr 24 14:30:07 2017 -0400 |
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| @@ -1,5 +1,5 @@ -<tool id="trim_galore" name="Trim Galore!" version="0.4.3" profile="17.01"> - <!-- Wrapper compatible with Trim Galore! version 0.4 --> +<tool id="trim_galore" name="Trim Galore!" version="0.4.3.0" profile="17.01"> + <!-- Wrapper compatible with Trim Galore! version 0.4.3 --> <description>Quality and adapter trimmer of reads</description> <macros> <macro name="adapter_trimming"> @@ -24,7 +24,6 @@ </conditional> </macro> <macro name="paired_adapter_trimming"> - <expand macro="adapter_trimming"> <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2"> <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator> @@ -44,16 +43,12 @@ </macro> </macros> <requirements> - <!-- conda dependency --> - <requirement type="package" version="1.8.3">cutadapt</requirement> - <requirement type="package" version="1.8">cutadapt</requirement> + <requirement type="package" version="0.4.3">trim-galore</requirement> </requirements> <version_command> - perl '$__tool_directory__/trim_galore' --version + trim_galore --version </version_command> - <command> -<![CDATA[ - + <command><![CDATA[ #set compressed = 'no' #if $singlePaired.sPaired == "single": #if $singlePaired.input_singles.is_of_type("fastq.gz"): @@ -95,7 +90,7 @@ ln -s '${singlePaired.input_mate_pairs.reverse}' ${read2} && #end if - perl '$__tool_directory__/trim_galore' + trim_galore ## we only support fastqsanger --phred33 @@ -146,13 +141,12 @@ #if $singlePaired.trimming.trimming_select == 'user': ## default 'AGATCGGAAGAGC' #if $singlePaired.trimming.adapter.strip() != '': - --adapter $singlePaired.trimming.adapter + --adapter '$singlePaired.trimming.adapter' #end if #else: $singlePaired.trimming.trimming_select #end if - #if $singlePaired.three_prime_clip_R1: --three_prime_clip_R1 $singlePaired.three_prime_clip_R1 #end if @@ -167,7 +161,7 @@ #if $singlePaired.trimming.trimming_select == 'user': #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '': - --adapter2 $singlePaired.trimming.adapter2 + --adapter2 '$singlePaired.trimming.adapter2' #end if #end if @@ -199,11 +193,9 @@ ## Trim Galore! run is finished. Move the report files to the proper place #if $params.settingsType == "custom" and $params.report: && - cat ./*_trimming_report.txt > $report_file; + cat ./*_trimming_report.txt > '$report_file' #end if - -]]> - </command> + ]]></command> <inputs> <!-- Input Parameters --> <conditional name="singlePaired"> @@ -283,8 +275,8 @@ label="Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs" /> </when> <!-- full --> </conditional> <!-- params --> + </inputs> - </inputs> <outputs> <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> @@ -331,8 +323,8 @@ <filter>params['settingsType'] == "custom"</filter> <filter>params['report'] == True</filter> </data> + </outputs> - </outputs> <tests> <test> <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> @@ -449,8 +441,7 @@ </output_collection> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ **What it does** `Trim Galore!`_ is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). It's main features are: @@ -473,7 +464,7 @@ * **Adapter sequence to be trimmed** * **Automatic detection** - + | Adapter sequence to be trimmed. Trim Galore will try to auto-detect whether the Illumina universal, Nextera transposase or Illumina small RNA adapter sequence was used. * **Illumina universal** @@ -518,7 +509,7 @@ | R2 <--------------------------- | | or this: - | + | | R1 -----------------------> | R2 <----------------- | @@ -600,7 +591,7 @@ | Selecting this option for non-directional RRBS libraries will screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs. Like with the option '--rrbs' this avoids using cytosine positions that were filled-in during the end-repair step. '--non_directional' requires '--rrbs' to be specified as well. | - | *option --non_directional*]]> - </help> + | *option --non_directional* + ]]></help> <citations></citations> </tool> |