Mercurial > repos > peterjc > mira_assembler
diff tools/mira3/mira.xml @ 10:a2fb1e67bd11 draft
Uploaded v0.0.9, correct path in dependency installation; renamed folder
| author | peterjc |
|---|---|
| date | Thu, 30 Jan 2014 13:21:21 -0500 |
| parents | |
| children | e59904c855ae |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mira3/mira.xml Thu Jan 30 13:21:21 2014 -0500 @@ -0,0 +1,191 @@ +<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8"> + <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> + <requirements> + <requirement type="binary">mira</requirement> + <requirement type="package" version="3.4.1.1">MIRA</requirement> + </requirements> + <version_command interpreter="python">mira.py -v</version_command> + <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log +##Give the wrapper script list of output filenames, then the mira command... +mira --job=$job_method,$job_type,$job_quality + +##Input files +#if $condBackbone.use == "true": + ## Can this be linked to job_method as well? If mapping we need the backbone... + -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename} +#end if +#if $condSanger.use == "true": + SANGER_SETTINGS + ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead + ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file + -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename} +#end if +#if $condRoche.use == "true": + 454_SETTINGS + ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead + ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file + -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename} +#end if +#if $condIllumina.use == "true": + SOLEXA_SETTINGS + ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead + -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename} + ##TODO - Look at -LR FASTQ qual offset (fqqo) +#end if +#if $condIonTorrent.use == "true": + IONTOR_SETTINGS + ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead + ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file + -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename} +#end if + +##Output files +COMMON_SETTINGS + +##ignore warnings about long read names +-MI:somrnl=0 + +##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output +##Explicitly disable formats we won't use like MAF (reduce IO) +-OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0 + +##remove_rollover_tmps, remove_tmp_directory +-OUT:rrot=1:rtd=1 + +##put mira temp directory on local storage +-DI:trt=/tmp + + </command> + <inputs> + <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)"> + <option value="denovo">De novo</option> + <option value="mapping">Mapping</option> + </param> + <param name="job_type" type="select" label="Assembly type"> + <option value="genome">Genome</option> + <option value="est">EST (transcriptome)</option> + </param> + <param name="job_quality" type="select" label="Assembly quality grade"> + <option value="accurate">Accurate</option> + <option value="normal">Normal (deprecated)</option> + <option value="draft">Draft</option> + </param> + <!-- Backbone --> + <conditional name="condBackbone"> + <param name="use" type="select" label="Backbones/reference chromosomes?" help="Required for mapping, optional for de novo assembly."> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false" /> + <when value="true"> + <!-- MIRA also allows CAF and GenBank, but Galaxy doesn't define those (yet) --> + <param name="filename" type="data" format="fasta" label="Backbone/reference sequences" help="FASTA format" /> + </when> + </conditional> + <!-- Sanger --> + <conditional name="condSanger"> + <param name="use" type="select" label="Sanger/Capillary reads?"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false" /> + <when value="true"> + <param name="filename" type="data" format="fastq" label="Sanger/Capillary reads file" help="FASTQ format" /> + </when> + </conditional> + <!-- Roche 454 --> + <conditional name="condRoche"> + <param name="use" type="select" label="454 reads?"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false" /> + <when value="true"> + <!-- TODO? Support SFF files directly, e.g. with sff_extract, but will need linker sequences --> + <param name="filename" type="data" format="fastq" label="Roche 454 reads file" help="FASTQ format" /> + </when> + </conditional> + <!-- Illumina --> + <conditional name="condIllumina"> + <param name="use" type="select" label="Solexa/Illumina reads?"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false" /> + <when value="true"> + <param name="filename" type="data" format="fastq" label="Solexa/Illumina reads file" help="FASTQ format" /> + </when> + </conditional> + <!-- Ion Torrent --> + <conditional name="condIonTorrent"> + <param name="use" type="select" label="Ion Torrent reads?"> + <option value="false">No</option> + <option value="true">Yes</option> + </param> + <when value="false" /> + <when value="true"> + <!-- TODO? Support SFF files directly, e.g. with sff_extract --> + <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" /> + </when> + </conditional> + </inputs> + <outputs> + <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" /> + <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" /> + <data name="out_caf" format="txt" label="MIRA contigs (CAF)" /> + <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> + <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> + <data name="out_log" format="txt" label="MIRA log" /> + </outputs> + <tests> + <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses + strain data and miraSearchESTSNPs. Here we just assemble it. --> +<!-- +Commenting out test until Galaxy framework is fixed, +https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests + <test> + <param name="job_method" value="denovo" /> + <param name="job_type" value="est" /> + <param name="job_qual" value="accurate" /> + <param name="condBackbone.use" value="false" /> + <param name="condSanger.use" value="true" /> + <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" /> + <param name="condRoche.use" value="false" /> + <param name="condIllumina.use" value="false" /> + <param name="condIonTorrent.use" value="false" /> + <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" /> + </test> +--> + </tests> + <help> + +**What it does** + +Runs MIRA v3.4, collects the output, and throws away all the temporary files. + +MIRA is an open source assembly tool capable of handling sequence data from +a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also +Ion Torrent). + +It is particularly suited to small genomes such as bacteria. + +**Citation** + +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 + +Bastien Chevreux, Thomas Wetter and Sándor Suhai (1999). +Genome Sequence Assembly Using Trace Signals and Additional Sequence Information. +Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56. +http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html + +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler + + </help> +</tool>