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Changeset 9:1bfc7254232e (2017-03-16)

Previous changeset 8:f1e71aeaa923 (2016-03-18) Next changeset 10:b4e39d993fc8 (2017-04-20)

Commit message:
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit f971832d2b34a182314e5201ea6895dd207c5923

modified:
trim_galore.xml

diff -r f1e71aeaa923 -r 1bfc7254232e trim_galore.xml
--- a/trim_galore.xml Fri Mar 18 07:56:01 2016 -0400
+++ b/trim_galore.xml Thu Mar 16 13:48:46 2017 -0400

b'@@ -1,15 +1,15 @@\n <tool id="trim_galore" name="Trim Galore!" version="0.4.2">\n \n- <description>adaptive quality and adapter trimmer</description>\n+ <description>Quality and adapter trimmer of reads</description>\n <macros>\n <macro name="adapter_trimming">\n <conditional name="trimming">\n- <param name="trimming_select" type="select" label="Trimming reads?">\n+ <param name="trimming_select" type="select" label="Adapter sequence to be trimmed">\n <option value="">Automatic detection</option>\n <option value="--illumina">Illumina universal</option>\n <option value="--nextera">Nextera transposase</option>\n <option value="--small_rna">Illumina small RNA adapters</option>\n- <option value="user">User defined adapter trimming</option>\n+ <option value="user">User defined adapter sequence</option>\n </param>\n <when value=""/>\n <when value="--illumina"/>\n@@ -36,10 +36,10 @@\n This may remove some unwanted bias from the 3\' end that is not directly related to adapter sequence or basecall quality.\n (--three_prime_clip_R1)</help>\n </param>\n- <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3\' end of read 1">\n+ <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3\' end of read 2">\n <help>Instructs Trim Galore! to remove N bp from the 3\' end of read 2 after\n adapter/quality trimming has been performed. This may remove some unwanted bias from\n- the 3\' end that is not directly related to adapter sequence or basecall quality. (--three_prime_clip_R2)</help>\n+ the 3\' end that is not directly related to adapter sequence or basecall quality.</help>\n </param>\n </macro>\n </macros>\n@@ -249,14 +249,14 @@\n <when value="default" />\n \n <when value="custom">\n- <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal"\n+ <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal (Enter phred quality score threshold)"\n help="For more information please see below." />\n <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" />\n <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" />\n- <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length INT" />\n+ <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length N" />\n \n- <param name="clip_R1" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove INT bp from the 5\' end of read 1" />\n- <param name="clip_R2" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove INT bp from the 5\' end of read 2" />\n+ <param name="clip_R1" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove N bp from the 5\' end of read 1" />\n+ <param name="clip_R2" type="integer" optional="True" min="0" label="Instructs Trim Galore! to remove N bp from the 5\' end of read 2 (Only for paired-end reads)" />\n \n <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" />\n \n@@ -287,7 +287,7 @@\n <param name'..b"is may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF.\n+ |\n+ | *option --three_prime_clip_R2*\n+\n+----\n+\n+**Advanced Settings**\n+\n+* **Trim low-quality ends from reads in addition to adapter removal**\n+\n+ | For RRBS samples, quality trimming will be performed first, and adapter trimming is carried in a second round. Other files are quality and adapter trimmed in a single pass. The algorithm is the same as the one used by BWA (Subtract <INT> from all qualities; compute partial sums from all indices to the end of the sequence; cut sequence at the index at which the sum is minimal). Default Phred score: 20.\n+ |\n+ | *option -q*\n+\n+* **Overlap with adapter sequence required to trim a sequence**\n+\n+ | Defaults to a very stringent setting of '1', i.e. even a single bp of overlapping sequence will be trimmed of the 3' end of any read.\n+ |\n+ | *option -s*\n+\n+* **Maximum allowed error rate**\n+\n+ | (no. of errors divided by the length of the matching region) (default: 0.1).\n+ |\n+ | *option -e*\n+\n+* **Discard reads that became shorter than length <INT>**\n+\n+ | because of either quality or adapter trimming. A value of '0' effectively disables this behaviour. Default: 20 bp.\n+ |\n+ | For paired-end files, both reads of a read-pair need to be longer than <INT> bp to be printed out to validated paired-end files (see option --paired). If only one read became too short there is the possibility of keeping such unpaired single-end reads (see --retain_unpaired). Default pair-cutoff: 20 bp.\n+ |\n+ | *option --length*\n+\n+* **Instructs Trim Galore! to remove INT bp from the 5' end of read 1**\n+\n+ | Instructs Trim Galore to remove <INT> bp from the 5' end of read 1 (or single-end reads). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end. Default: OFF.\n+ |\n+ | *option --clip_R1*\n+\n+* **Instructs Trim Galore! to remove INT bp from the 5' end of read 2**\n+\n+ | Instructs Trim Galore to remove <int> bp from the 5' end of read 2 (paired-end reads only). This may be useful if the qualities were very poor, or if there is some sort of unwanted bias at the 5' end. For paired-end BS-Seq, it is recommended to remove the first few bp because the end-repair reaction may introduce a bias towards low methylation. Please refer to the M-bias plot section in the Bismark User Guide for some examples. Default: OFF.\n+ |\n+ | *option --clip_R2*\n+\n+* **Specify if you would like to retain unpaired reads**\n+\n+ | If only one of the two paired-end reads became too short, the longer read will be written to either '.unpaired_1.fq' or '.unpaired_2.fq' output files. The length cutoff for unpaired single-end reads is governed by the parameters -r1/--length_1 and -r2/--length_2. Default: OFF.\n+ |\n+ | *option --retained_unpaired*\n+\n+----\n+\n+**RRBS specific settings**\n+\n+* **Specifies that the input file was an MspI digested RRBS sample (recognition site: CCGG)**\n+\n+ | Sequences which were adapter-trimmed will have a further 2 bp removed from their 3' end. This is to avoid that the filled-in C close to the second MspI site in a sequence is used for methylation calls. Sequences which were merely trimmed because of poor quality will not be shortened further.\n+ |\n+ | *option -rrbs*\n+\n+* **Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs**\n+\n+ | 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.\n+ |\n+ | *option --non_directional*]]>\n </help>\n <citations></citations>\n </tool>\n"