Mercurial > repos > bgruening > trim_galore
diff trim_galore.xml @ 6:11962ce40855 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/trim_galore commit 9198b904ef37fe46007256f1734c33de6d23331b-dirty
author | bgruening |
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date | Wed, 07 Oct 2015 08:39:59 -0400 |
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children | 8352713cf939 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trim_galore.xml Wed Oct 07 08:39:59 2015 -0400 @@ -0,0 +1,372 @@ +<tool id="trim_galore" name="Trim Galore!" version="0.4.0"> + <!-- Wrapper compatible with Trim Galore! version 0.4 --> + <description>adaptive quality and adapter trimmer</description> + <macros> + <macro name="adapter_trimming"> + <conditional name="trimming"> + <param name="trimming_select" type="select" label="Trimming reads?"> + <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> + </param> + <when value="auto"/> + <when value="--illumina"/> + <when value="--nextera"/> + <when value="--small_rna"/> + <when value="user"> + <param name="adapter" type="text" value="AGATCGGAAGAGC" label="Adapter sequence to be trimmed off"> + <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator> + </param> + <yield/> + </when> + </conditional> + </macro> + <macro name="paired_adapter_trimming"> + + <expand macro="adapter_trimming"> + <param name="adapter2" type="text" optional="True" value="" label="Adapter sequence to be trimmed off read 2"> + <validator type="regex" message="Adapter sequence must contain DNA characters only (A,C,T,G or N)">^[ACTGNactgn]*$</validator> + </param> + </expand> + <param name="trim1" type="boolean" truevalue="--trim1" falsevalue="" checked="False" label="Trims 1 bp off every read from its 3' end." help="" /> + <param name="three_prime_clip_R1" type="integer" value="" optional="True" label="Remove N bp from the 3' end of read 1"> + <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. + (--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"> + <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> + </param> + </macro> + </macros> + <requirements> + <requirement type="package" version="1.8">cutadapt</requirement> + </requirements> + <version_command interpreter="perl">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 + + #if $singlePaired.sPaired == "single": + ln -s "${singlePaired.input_singles}" ./input_singles; + #elif $singlePaired.sPaired == "paired": + ln -s "${singlePaired.input_mate1}" ./input_mate1; + ln -s "${singlePaired.input_mate2}" ./input_mate2; + #else: + ln -s "${singlePaired.input_mate_pairs.forward}" ./input_mate1; + ln -s "${singlePaired.input_mate_pairs.reverse}" ./input_mate2; + #end if + + perl $__tool_directory__/trim_galore + + ## we only support fastqsanger + --phred33 + + #if $params.settingsType == "custom": + + ## default 20 + --quality $params.quality + + ## default 1 + --stringency $params.stringency + + ## default 0.1 + -e $params.error_rate + + ## default 20 + --length $params.min_length + + #if $params.clip_R1: + --clip_R1 $params.clip_R1 + #end if + + #if $params.clip_R2: + --clip_R2 $params.clip_R2 + #end if + + #if $params.retain_unpaired.retain_unpaired_select == "retain_unpaired_output": + --retain_unpaired + --length_1 $params.retain_unpaired.length_1 + --length_2 $params.retain_unpaired.length_2 + #end if + + #end if + + ## RBBS specific options. + #if $rrbs.settingsType == "custom": + $rrbs.rrbs + $rrbs.non_directional + #end if + + --output_dir ./ + --suppress_warn + + #if $params.settingsType == "custom" and not $params.report: + --no_report_file + #end if + + #if $singlePaired.trimming.trimming_select == 'user': + ## default 'AGATCGGAAGAGC' + #if $singlePaired.trimming.adapter.strip() != '': + --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 + + #if $singlePaired.sPaired == "single": + ## input sequence + ./input_singles + #else: + --paired + + $singlePaired.trim1 + + #if $singlePaired.trimming.trimming_select == 'user': + #if $singlePaired.trimming.adapter2 and $singlePaired.trimming.adapter2.strip() != '': + --adapter2 $singlePaired.trimming.adapter2 + #end if + #end if + + #if $singlePaired.three_prime_clip_R2: + --three_prime_clip_R2 $singlePaired.three_prime_clip_R2 + #end if + + ## input sequences + ./input_mate1 + ./input_mate2 + + #end if + + ## 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; + #end if + +]]> + </command> + <inputs> + <!-- Input Parameters --> + <conditional name="singlePaired"> + <param name="sPaired" type="select" label="Is this library paired- or single-end?"> + <option value="single">Single-end</option> + <option value="paired">Paired-end</option> + <option value="paired_collection">Paired Collection</option> + </param> + <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. + (--three_prime_clip_R1)</help> + </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" /> + <expand macro="paired_adapter_trimming" /> + </when> + <when value="paired_collection"> + <param name="input_mate_pairs" format="fastqsanger" 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> + </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> + <option value="custom">Full parameter list</option> + </param> + <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" + 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="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="report" type="boolean" truevalue="true" falsevalue="false" checked="False" label="Generate a report file" help="" /> + + <conditional name="retain_unpaired"> + <param name="retain_unpaired_select" type="select" label="specify if you would like to retain unpaired reads"> + <option value="no_output">Do not output unpaired reads</option> + <option value="retain_unpaired_output">Output unpaired reads</option> + </param> + <when value="no_output" /> + <!-- Output params. --> + <when value="retain_unpaired_output"> + <param name="length_1" type="integer" value="35" label="Unpaired single-end read length cutoff needed for read 1 to be written" /> + <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 --> + + <conditional name="rrbs"> + <param name="settingsType" type="select" label="RRBS specific settings"> + <option value="default">Use defaults (no RRBS)</option> + <option value="custom">Full parameter list</option> + </param> + <when value="default" /> + <!-- Full/advanced params. --> + <when value="custom"> + <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" /> + </when> <!-- full --> + </conditional> <!-- params --> + + </inputs> + <outputs> + <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 ${on_string}: unpaired reads"> + <data name="forward" format="fastqsanger" from_work_dir="input_mate1_unpaired_1.fq" /> + <data name="reverse" format="fastqsanger" from_work_dir="input_mate2_unpaired_2.fq" /> + <filter>params['settingsType'] == "custom"</filter> + <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> + <filter>singlePaired['sPaired'] == "paired_collection"</filter> + </collection> + + <data format="fastqsanger" name="trimmed_reads_pair1" from_work_dir="input_mate1_val_1.fq" + label="${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 ${on_string}: trimmed reads pair 2"> + <filter>singlePaired['sPaired'] == "paired"</filter> + </data> + + <data format="fastqsanger" name="unpaired_reads_1" from_work_dir="input_mate1_val_1.fq" + label="${tool.name} on ${on_string}: unpaired reads (1)"> + <filter>params['settingsType'] == "custom"</filter> + <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> + <filter>singlePaired['sPaired'] == "paired"</filter> + </data> + + <data format="fastqsanger" name="unpaired_reads_2" from_work_dir="input_mate2_val_2.fq" + label="${tool.name} on ${on_string}: unpaired reads (2)"> + <filter>params['settingsType'] == "custom"</filter> + <filter>params['retain_unpaired']['retain_unpaired_select'] == "retain_unpaired_output"</filter> + <filter>singlePaired['sPaired'] == "paired"</filter> + </data> + <data format="txt" name="report_file" label="${tool.name} on ${on_string}: report file"> + <filter>params['settingsType'] == "custom"</filter> + <filter>params['report'] == True</filter> + </data> + + </outputs> + <tests> + <test> + <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <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.fastqsanger" ftype="fastqsanger"/> + <output name="report_file" file="sanger_full_range_report_results1.txt" ftype="txt" lines_diff="2" /> + </test> + + <test> + <param name="input_singles" value="sanger_full_range_original_sanger.fastqsanger" ftype="fastqsanger" /> + <param name="sPaired" value="single" /> + <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.fastqsanger" ftype="fastqsanger" /> + <param name="sPaired" value="single" /> + <param name="adapter" value="AAAGAGC" /> + <output name="trimmed_reads_single" file="sanger_full_range_results3.fastqsanger" ftype="fastqsanger"/> + </test> + + <test> + <param name="input_mate1" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> + <param name="input_mate2" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> + <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.fastqsanger" ftype="fastqsanger"/> + <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="8" /> + </test> + + <test> + <param name="input_mate_pairs"> + <collection type="paired"> + <element name="forward" value="bwa-mem-fastq1.fq" ftype="fastqsanger" /> + <element name="reverse" value="bwa-mem-fastq2.fq" ftype="fastqsanger" /> + </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_results3.txt" ftype="txt" lines_diff="8" /> + + <output_collection name="trimmed_reads_paired_collection" type="paired"> + <element name="forward" file="paired_collection_example_pair1_results3.fastqsanger" ftype="fastqsanger"/> + <element name="reverse" file="paired_collection_example_pair2_results3.fastqsanger" ftype="fastqsanger"/> + </output_collection> + + <output_collection name="trimmed_reads_unpaired_collection" type="paired"> + <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> + </tests> + <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: + + * For adapter trimming, Trim Galore! uses the first 13 bp of Illumina standard adapters ('AGATCGGAAGAGC') by default (suitable for both ends of paired-end libraries), but accepts other adapter sequence, too + * For MspI-digested RRBS libraries, Trim Galore! performs quality and adapter trimming in two subsequent steps. This allows it to remove 2 additional bases that contain a cytosine which was artificially introduced in the end-repair step during the library preparation + * For any kind of FASTQ file other than MspI-digested RRBS, Trim Galore! can perform single-pass adapter and quality trimming + * The Phred quality of basecalls and the stringency for adapter removal can be specified individually + * Trim Galore! can remove sequences if they become too short during the trimming process. For paired-end files Trim Galore! removes entire sequence pairs if one (or both) of the two reads became shorter than the set length cutoff. Reads of a read-pair that are longer than a given threshold but for which the partner read has become too short can optionally be written out to single-end files. This ensures that the information of a read pair is not lost entirely if only one read is of good quality + * Trim Galore! can trim paired-end files by 1 additional bp from the 3' end of all reads to avoid problems with invalid alignments with Bowtie 1 + +.. _Trim Galore!: http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ + +It is developed by Felix Krueger at the Babraham Institute. +]]> + </help> + <citations></citations> +</tool>