Mercurial > repos > bgruening > trim_galore
changeset 9:383e9f2eaa6c draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 93babf3018c7291d11206999ba82750f8def33c6
| author | bgruening |
|---|---|
| date | Wed, 09 Nov 2016 14:36:33 -0500 |
| parents | d5dbba73786b |
| children | 02efbf4740c1 |
| files | trim_galore.xml |
| diffstat | 1 files changed, 162 insertions(+), 11 deletions(-) [+] |
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--- a/trim_galore.xml Tue Mar 29 12:20:39 2016 -0400 +++ b/trim_galore.xml Wed Nov 09 14:36:33 2016 -0500 @@ -1,15 +1,15 @@ <tool id="trim_galore" name="Trim Galore!" version="0.4.2"> <!-- Wrapper compatible with Trim Galore! version 0.4 --> - <description>adaptive quality and adapter trimmer</description> + <description>Quality and adapter trimmer of reads</description> <macros> <macro name="adapter_trimming"> <conditional name="trimming"> - <param name="trimming_select" type="select" label="Trimming reads?"> + <param name="trimming_select" type="select" label="Adapter sequence to be trimmed"> <option value="">Automatic detection</option> <option value="--illumina">Illumina universal</option> <option value="--nextera">Nextera transposase</option> <option value="--small_rna">Illumina small RNA adapters</option> - <option value="user">User defined adapter trimming</option> + <option value="user">User defined adapter sequence</option> </param> <when value=""/> <when value="--illumina"/> @@ -24,6 +24,7 @@ </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> @@ -35,10 +36,10 @@ This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. (--three_prime_clip_R1)</help> </param> - <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1"> + <param name="three_prime_clip_R2" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 2"> <help>Instructs Trim Galore! to remove N bp from the 3' end of read 2 after adapter/quality trimming has been performed. This may remove some unwanted bias from - the 3' end that is not directly related to adapter sequence or basecall quality. (--three_prime_clip_R2)</help> + the 3' end that is not directly related to adapter sequence or basecall quality.</help> </param> </macro> </macros> @@ -52,6 +53,7 @@ </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. @@ -113,6 +115,7 @@ --length_1 $params.retain_unpaired.length_1 --length_2 $params.retain_unpaired.length_2 #end if + #end if ## RBBS specific options. @@ -137,6 +140,7 @@ $singlePaired.trimming.trimming_select #end if + #if $singlePaired.three_prime_clip_R1: --three_prime_clip_R1 $singlePaired.three_prime_clip_R1 #end if @@ -204,6 +208,7 @@ && cat ./*_trimming_report.txt > $report_file; #end if + ]]> </command> <inputs> @@ -217,6 +222,7 @@ <when value="single"> <param name="input_singles" type="data" format="fastqsanger" 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"> <help>Instructs Trim Galore! to remove N bp from the 3' end of read 1 after adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. @@ -234,6 +240,7 @@ <expand macro="paired_adapter_trimming" /> </when> </conditional> + <conditional name="params"> <param name="settingsType" type="select" label="Trim Galore! advanced settings" help="You can use the default settings or set custom values for any of Trim Galore!'s parameters."> <option value="default">Use defaults</option> @@ -242,14 +249,15 @@ <when value="default" /> <!-- Full/advanced params. --> <when value="custom"> - <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal" + <param name="quality" type="integer" value="20" label="Trim low-quality ends from reads in addition to adapter removal (Enter phred quality score threshold)" help="For more information please see below." /> <param name="stringency" type="integer" value="1" label="Overlap with adapter sequence required to trim a sequence" /> <param name="error_rate" type="float" value="0.1" label="Maximum allowed error rate" /> - <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length INT" /> + <param name="min_length" type="integer" value="20" label="Discard reads that became shorter than length 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" /> - <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" /> + <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" /> + <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)" /> + <param name="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" /> <conditional name="retain_unpaired"> @@ -264,6 +272,7 @@ <param name="length_2" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 2 to be written" /> </when> <!-- output --> </conditional> <!-- retain_unpaired --> + </when> <!-- full --> </conditional> <!-- params --> @@ -278,7 +287,7 @@ <param name="rrbs" type="boolean" truevalue="--rrbs" falsevalue="" checked="True" label="Specifies that the input file was an MspI digested RRBS sample" /> <param name="non_directional" type="boolean" truevalue="--non_directional" falsevalue="" checked="False" - label="Selecting this option for non-directional RRBS libraries" /> + 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 --> @@ -287,11 +296,13 @@ <data format="fastqsanger" name="trimmed_reads_single" from_work_dir="input_singles_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 ${on_string}: paired reads"> <data name="forward" format="fastqsanger" from_work_dir="input_mate1_val_1.fq" /> <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_val_2.fq" /> <filter>singlePaired['sPaired'] == "paired_collection"</filter> </collection> + <collection name="trimmed_reads_unpaired_collection" type="paired" label="${tool.name} on ${on_string}: unpaired reads"> <data name="forward" format="fastqsanger" from_work_dir="input_mate1_unpaired_1.fq" /> <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_unpaired_2.fq" /> @@ -299,20 +310,24 @@ <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> <filter>singlePaired['sPaired'] == "paired_collection"</filter> </collection> + <data format="fastqsanger" name="trimmed_reads_pair1" from_work_dir="input_mate1_val_1.fq" label="${tool.name} on ${on_string}: trimmed reads pair 1"> <filter>singlePaired['sPaired'] == "paired"</filter> </data> + <data format="fastqsanger" name="trimmed_reads_pair2" from_work_dir="input_mate2_val_2.fq" label="${tool.name} on ${on_string}: trimmed reads pair 2"> <filter>singlePaired['sPaired'] == "paired"</filter> </data> + <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_unpaired_1.fq" label="${tool.name} on ${on_string}: unpaired reads (1)"> <filter>params['settingsType'] == "custom"</filter> <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> <filter>singlePaired['sPaired'] == "paired"</filter> </data> + <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_unpaired_2.fq" label="${tool.name} on ${on_string}: unpaired reads (2)"> <filter>params['settingsType'] == "custom"</filter> @@ -323,6 +338,7 @@ <filter>params['settingsType'] == "custom"</filter> <filter>params['report'] == True</filter> </data> + </outputs> <tests> <test> @@ -402,7 +418,142 @@ .. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ It is developed by Felix Krueger at the Babraham Institute. -]]> + +---- + +**Main Settings** + +* **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** + + | Adapter sequence to be trimmed is the first 13bp of the Illumina universal adapter 'AGATCGGAAGAGC' instead of the default auto-detection of adapter sequence. + | + | *option --illumina* + + * **Nextera transposase** + + | Adapter sequence to be trimmed is the first 12bp of the Nextera adapter 'CTGTCTCTTATA' instead of the default auto-detection of adapter sequence. + | + | *option --nextera* + + * **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. + | + | *option --small_rna* + + * **User defined adapter trimming** + + | Adapter sequence to be trimmed is the sequence entered by the user instead of the default auto-detection of adapter sequence. + | + | *option -a* + +* **If Single-End Reads** + + * **Remove <int> bp from the 3' end** + + | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF. + | + | *option --three_prime_clip_R1* + +* **If Paired-End Reads** + + * **Trims 1 bp off every read from its 3' end** + + | This may be needed for FastQ files that are to be aligned as paired-end data with Bowtie. This is because Bowtie (1) regards alignments like this: + | + | R1 ---------------------------> + | R2 <--------------------------- + | + | or this: + | + | R1 -----------------------> + | R2 <----------------- + | + | as invalid (whenever a start/end coordinate is contained within the other read). + | + | *option --t* + + * **Remove <int> bp from the 3' end of read 1** + + | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 1 (or single-end reads) AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF. + | + | *option --three_prime_clip_R1* + + * **Remove <int> bp from the 3' end of read 2** + + | <int> Instructs Trim Galore to remove <int> bp from the 3' end of read 2 AFTER adapter/quality trimming has been performed. This may remove some unwanted bias from the 3' end that is not directly related to adapter sequence or basecall quality. Default: OFF. + | + | *option --three_prime_clip_R2* + +---- + +**Advanced Settings** + +* **Trim low-quality ends from reads in addition to adapter removal** + + | 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. + | + | *option -q* + +* **Overlap with adapter sequence required to trim a sequence** + + | 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. + | + | *option -s* + +* **Maximum allowed error rate** + + | (no. of errors divided by the length of the matching region) (default: 0.1). + | + | *option -e* + +* **Discard reads that became shorter than length <INT>** + + | because of either quality or adapter trimming. A value of '0' effectively disables this behaviour. Default: 20 bp. + | + | 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. + | + | *option --length* + +* **Instructs Trim Galore! to remove INT bp from the 5' end of read 1** + + | 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. + | + | *option --clip_R1* + +* **Instructs Trim Galore! to remove INT bp from the 5' end of read 2** + + | 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. + | + | *option --clip_R2* + +* **Specify if you would like to retain unpaired reads** + + | 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. + | + | *option --retained_unpaired* + +---- + +**RRBS specific settings** + +* **Specifies that the input file was an MspI digested RRBS sample (recognition site: CCGG)** + + | 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. + | + | *option -rrbs* + +* **Screen quality-trimmed sequences for 'CAA' or 'CGA' at the start of the read and, if found, removes the first two basepairs** + + | 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> <citations></citations> </tool>