Mercurial > repos > artbio > sr_bowtie
diff sRbowtie.xml @ 0:de9cd3998571 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/sr_bowtie commit 19d31884000f86a5e5e07cd98ecd29fe6c9b1a7e
| author | artbio |
|---|---|
| date | Sat, 02 Sep 2017 10:52:05 -0400 |
| parents | |
| children | 5f4fbba31b6a |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/sRbowtie.xml Sat Sep 02 10:52:05 2017 -0400 @@ -0,0 +1,283 @@ +<tool id="bowtieForSmallRNA" name="sR_bowtie" version="2.0.0"> + <description>for small RNA short reads</description> + <requirements> + <requirement type="package" version="1.1.2=py27_2">bowtie</requirement> + <requirement type="package" version="1.2">samtools</requirement> + </requirements> + <command detect_errors="exit_code"><![CDATA[ + #if $refGenomeSource.genomeSource == "history": + bowtie-build -f $refGenomeSource.ownFile genome && + ln -s -f '$refGenomeSource.ownFile' genome.fa && + #set index_path = 'genome' + #else: + #set index_path = $refGenomeSource.index.fields.path + #end if + #if $input.extension == "fasta": + #set format = "-f" + #elif $input.extension == "fastq": + #set format = "-q" + #end if + + ## set the method_prefix + #if $method == "RNA": + #set method_prefix = "-v %s -M 1 --best --strata --norc" % str($v_mismatches) + #elif $method == "unique": + #set method_prefix = "-v %s -m 1" % str($v_mismatches) + #elif $method == "multiple": + #set method_prefix = "-v %s -M 1 --best --strata" % str($v_mismatches) + #elif $method == "k_option": + #set method_prefix = "-v %s -k 1 --best" % str($v_mismatches) + #elif $method == "n_option": + #set method_prefix = "-n %s -M 1 --best" % str($v_mismatches) + #elif $method == "a_option": + #set method_prefix = "-v %s -a --best" % str($v_mismatches) + #end if + + ## set the extra_output + #if $additional_fasta == "No": + #set extra_output = "" + #elif $additional_fasta == "al": + #set extra_output = " --al %s " % str($aligned) + #elif $additional_fasta == "unal": + #set extra_output = " --un %s " % str($unaligned) + #else: + #set extra_output = " --al %s --un %s " % (str($aligned), str($unaligned)) + #end if + + #set $method_postfix = " %s %s " % ($method_prefix, $extra_output) + + ## run the bowtie alignement + #if $output_format == "tabular": + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix --suppress 6,7,8 $index_path $format '$input' > $output + #elif $output_format == "sam": + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' > '$output' + #elif $output_format == "bam": + bowtie -p \${GALAXY_SLOTS:-4} $method_postfix -S $index_path $format '$input' | samtools view -u - | samtools sort -@ "\${GALAXY_SLOTS:-4}" -T tmp -O bam -o $output + #end if + ##### | samtools view -uS + ]]></command> + <inputs> + <param format="fasta, fastq" help="Only with clipped, fasta or fastq read files" label="Input fasta or fastq file: reads clipped from their adapter" name="input" type="data" /> + <param help="bowtie parameters adjusted to the type of matching. RNA option match to only one strand" label="What kind of matching do you want to do?" name="method" type="select"> + <option value="RNA">Match on sense strand RNA reference index, multiple mappers randomly matched at a single position</option> + <option value="unique">Match unique mappers on DNA reference index</option> + <option selected="true" value="multiple">Match on DNA, multiple mappers randomly matched at a single position</option> + <option value="k_option">Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)</option> + <option value="n_option">Match on DNA - RNAseq mode (-n bowtie option)</option> + <option value="a_option">Match and report all valid alignments</option> + </param> + <param help="specify the -v bowtie option" label="Number of mismatches allowed" name="v_mismatches" type="select"> + <option value="0">0</option> + <option selected="true" value="1">1</option> + <option value="2">2</option> + <option value="3">3</option> + </param> + <conditional name="refGenomeSource"> + <param help="Built-ins were indexed using default options" label="Will you select a reference genome from your history or use a built-in index?" name="genomeSource" type="select"> + <option value="indexed">Use a built-in index</option> + <option value="history">Use one from the history</option> + </param> + <when value="indexed"> + <param help="if your genome of interest is not listed - contact instance administrator" label="Select a DNA reference index" name="index" type="select"> + <options from_data_table="bowtie_indexes"> + + </options> + </param> + </when> + <when value="history"> + <param format="fasta" label="Select a fasta file, to serve as index reference" name="ownFile" type="data" /> + </when> + </conditional> + <param help="Note that the BAM will be viewable in trackster only if you choose a full genome referenced for Trackster usage. see the doc below" label="Select output format" name="output_format" type="select"> + <option selected="true" value="tabular">tabular</option> + <option value="sam">sam</option> + <option value="bam">bam</option> + </param> + <param help="to get aligned and unaligned reads in fasta format" label="additional fasta output" name="additional_fasta" type="select"> + <option selected="true" value="No">No</option> + <option value="al">aligned</option> + <option value="unal">unaligned</option> + <option value="al_and_unal">both aligned and unaligned</option> + </param> + </inputs> + <outputs> + <data format="tabular" label="Bowtie Output" name="output"> + <change_format> + <when format="sam" input="output_format" value="sam" /> + <when format="bam" input="output_format" value="bam" /> + </change_format> + <actions> + <conditional name="refGenomeSource.genomeSource"> + <when value="indexed"> + <action name="dbkey" type="metadata"> + <option column="1" name="bowtie_indexes" offset="0" type="from_data_table"> + <filter column="0" compare="startswith" keep="False" type="param_value" value="#" /> + <filter column="0" ref="refGenomeSource.index" type="param_value" /> + </option> + </action> + </when> + <when value="history"> + <action name="dbkey" type="metadata"> + <option name="refGenomeSource.ownFile" param_attribute="dbkey" type="from_param" /> + </action> + </when> + </conditional> + </actions> + </data> + <data format="fasta" label="Matched reads" name="aligned"> + <filter>additional_fasta == "al" or additional_fasta == "al_and_unal"</filter> + </data> + <data format="fasta" label="Unmatched reads" name="unaligned"> + <filter>additional_fasta == "unal" or additional_fasta == "al_and_unal"</filter> + </data> + </outputs> + <tests> + <test> + <param name="genomeSource" value="history" /> + <param ftype="fasta" name="ownFile" value="297_reference.fa" /> + <param name="method" value="unique" /> + <param ftype="fasta" name="input" value="input.fa" /> + <param name="v_mismatches" value="1" /> + <param name="output_format" value="bam" /> + <output file="output.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> + </test> + <test> + <param name="genomeSource" value="history" /> + <param ftype="fasta" name="ownFile" value="297_reference.fa" /> + <param name="method" value="unique" /> + <param ftype="fastq" name="input" value="input.fastq" /> + <param name="v_mismatches" value="1" /> + <param name="output_format" value="bam" /> + <output file="output2.bam" ftype="bam" compare="sim_size" delta="1000" name="output" /> + </test> + <test> + <param name="genomeSource" value="history" /> + <param ftype="fasta" name="ownFile" value="297_reference.fa" /> + <param name="method" value="multiple" /> + <param ftype="fasta" name="input" value="input.fa" /> + <param name="v_mismatches" value="1" /> + <param name="output_format" value="tabular" /> + <output file="output.tab" ftype="tabular" name="output" /> + </test> + <test> + <param name="genomeSource" value="history" /> + <param ftype="fasta" name="ownFile" value="297_reference.fa" /> + <param name="method" value="multiple" /> + <param ftype="fasta" name="input" value="input.fa" /> + <param name="v_mismatches" value="1" /> + <param name="additional_fasta" value="al" /> + <param name="output_format" value="tabular" /> + <output file="output.tab" ftype="tabular" name="output" /> + <output file="al.fa" ftype="fasta" name="aligned" /> + </test> + </tests> + <help> + +**What it does** + +Bowtie_ is a short read aligner designed to be ultrafast and memory-efficient. It is developed by Ben Langmead and Cole Trapnell. Please cite: Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10:R25. + +.. _Bowtie: http://bowtie-bio.sourceforge.net/index.shtml + +A generic "Map with Bowtie for Illumina" Galaxy tool is available in the main Galaxy distribution. + +However, this Bowtie wrapper tool only takes FASTQ files as inputs. + +The sRbowtie wrapper works with short (-v bowtie mode) reads inputs, in fasta or fastq format, and proposes a simplified set of configurations suited to small RNA analysis. + +------ + +**OPTIONS** + +.. class:: infomark + +This script uses Bowtie to match reads on a reference index. + +Depending on the type of matching, different bowtie options are used: + +**Match on sense strand RNA reference index, multiple mappers randomly matched at a single position** + +Align on RNA reference, SENSE strand, randomly attributing multiple mapper to target with least mismatches: + +*-v [0,1,2,3] -M 1 --best --strata -p 12 --norc* + +**Match unique mappers on DNA reference index** + +Align ONLY unique mappers on DNA reference index + +*-v [0,1,2,3] -m 1 -p 12* + +Note that using this option with -v values other than 0 is questionnable... + +**Match on DNA, multiple mappers randomly matched at a single position** + +Align multiple mappers, randomly attributing multiple mapper to target with least mismatches, number of mismatch allowed specified by -v option: + +*-v [0,1,2,3] -M 1 --best --strata -p 12* + +**Match on DNA as fast as possible, without taking care of mapping issues (for raw annotation of reads)** + +Align with highest speed, not guaranteeing best hit for speed gain: + +*-v [0,1,2,3] -k 1 --best -p 12* + +**Match on DNA - RNAseq mode (-n bowtie option)** + +Align reads in as for RNAseq data alignment + +*-n [0,1,2,3] -M 1 --best -p 12* + +**Match and report all valid alignments** + +Align reads and report all valid alignments + +*-v [0,1,2,3] -a --best -p 12* + + + +----- + +**Input formats** + +.. class:: warningmark + +*Lists of reads, in fasta or fastq format, clipped from their adapter sequence* + +----- + +**OUTPUTS** + +If you choose tabular as the output format, you will obtain the matched reads in tabular bowtie output format (--suppress 6,7,8), having the following columns:: + + Column Description + -------- -------------------------------------------------------- + 1 FastaID fasta identifier + 2 polarity + or - depending whether the match was reported on the forward or reverse strand + 3 target name of the matched target + 4 Offset O-based coordinate of the miR on the miRBase pre-miR sequence + 5 Seq sequence of the matched Read + +If you choose SAM, you will get the output in unordered SAM format. + +.. class:: warningmark + +if you choose BAM, the output will be in sorted BAM format. +To be viewable in Trackster, several condition must be fulfilled: + +.. class:: infomark + +Reads must have been matched to a genome whose chromosome names are compatible with Trackster genome indexes + +.. class:: infomark + +the database/Build (dbkey) which is indicated for the dataset (Pencil - Database/Build field) must match a Trackster genome index. + +Please contact the Galaxy instance administrator if your genome is not referenced + +**Matched and unmatched fasta reads can be retrieved, for further analyses** + + </help> + <citations> + <citation type="doi">10.1186/gb-2009-10-3-r25</citation> + </citations> +</tool>