Mercurial > repos > peterjc > mira4_assembler
diff tools/mira4_assembler/mira4_de_novo.xml @ 1:70248e6e3efc draft
v0.0.7 move dependency to package_mira_4_0_2 etc
| author | peterjc |
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| date | Wed, 05 Aug 2015 11:31:05 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mira4_assembler/mira4_de_novo.xml Wed Aug 05 11:31:05 2015 -0400 @@ -0,0 +1,275 @@ +<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.7"> + <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description> + <requirements> + <requirement type="binary">mira</requirement> + <requirement type="binary">miraconvert</requirement> + <requirement type="package" version="4.0.2">MIRA</requirement> + <requirement type="binary">samtools</requirement> + <requirement type="package" version="0.1.19">samtools</requirement> + </requirements> + <code file="mira4_validator.py" /> + <stdio> + <!-- Assume anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + </stdio> + <version_command interpreter="python">mira4.py --version</version_command> + <command interpreter="python">mira4.py +--manifest "$manifest" +#if str($maf_wanted)=="true": +--maf "$out_maf" +#end if +#if str($bam_wanted)=="true": +--bam "$out_bam" +#end if +--fasta "$out_fasta" +--log "$out_log" + </command> + <configfiles> + <configfile name="manifest"> +project = MIRA +job = denovo,${job_type},${job_quality} +parameters = -NW:cmrnl=no -DI:trt=/tmp -OUT:orc=no +## -GE:not is short for -GENERAL:number_of_threads and using one (1) +## can be useful for repeatability of assemblies and bug hunting. +## This is overriden by the command line -t switch which is easier +## to set from within Galaxy. +## +## -NW:cmrnl is short for -NAG_AND_WARN:check_maxreadnamelength +## and without this MIRA aborts with read names over 40 characters +## due to limitations of some downstream tools. +## +## -DI:trt is short for -DIRECTORY:tmp_redirected_to and should +## point to a local hard drive (not something like NFS on network). +## We replace /tmp with an environment variable via mira4.py +## +## -OUT:orc=no is short for -OUTPUT:output_result_caf=no +## which turns off an output file we don't want anyway. + +#for $rg in $read_group + +##This bar goes into the manifest as a comment line +#------------------------------------------------------------------------------ + +readgroup +technology = ${rg.technology} +##Record the segment placement (if any) +#if str($rg.segments.type) == "paired" +segment_placement = ${rg.segments.placement} +segment_naming = ${rg.segments.naming} +#if str($rg.segments.min_size) != "" or str($rg.segments.max_size) != "" +##If our min/max validation failed I trust MIRA to give an error message... +template_size = $rg.segments.min_size $rg.segments.max_size +#end if +#end if +##if str($rg.segments.type) == "none" +##MIRA4 manual says use segment_placement = unknown or ? for unpaired data +##but this stopped working in MIRA 4.0 RC5 and 4.0 (final). See: +##http://www.freelists.org/post/mira_talk/Unpaired-reads-and-segment-placement--or-unknown +##segment_placement = ? +##end if +##MIRA will accept multiple filenames on one data line, or multiple data lines +#for $f in $rg.filenames +##Must now map Galaxy datatypes to MIRA file types... +#if $f.ext.startswith("fastq") +##MIRA doesn't like fastqsanger etc, just plain old fastq: +data = fastq::$f +#elif $f.ext == "mira" +##We're calling *.maf the "mira" format in Galaxy (name space collision) +data = maf::$f +#else +##MIRA is happy with fasta as name, +data = ${f.ext}::$f +#end if +#end for +#end for + </configfile> + </configfiles> + <inputs> + <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="draft">Draft</option> + </param> + <repeat name="read_group" title="Read Group" min="1"> + <param name="technology" type="select" label="Read technology"> + <option value="solexa">Solexa/Illumina</option> + <option value="sanger">Sanger cappillary sequencing</option> + <option value="454">Roche 454</option> + <option value="iontor">Ion Torrent</option> + <option value="pcbiolq">PacBio low quality (raw)</option> + <option value="pcbiohq">PacBio high quality (corrected)</option> + <option value="text">Synthetic reads (database entries, consensus sequences, artifical reads, etc)</option> + <!-- TODO reference/backbone as an entry here? --> + </param> + <conditional name="segments"> + <param name="type" type="select" label="Are these paired reads?"> + <option value="paired">Paired reads</option> + <option value="none">Single reads or not relevant (e.g. primer walking with Sanger capillary sequencing)</option> + </param> + <when value="paired"> + <param name="placement" type="select" label="Pairing type (segment placing)"> + <option value="FR">---> <--- (e.g. Sanger capillary or Solexa/Illumina paired-end library)</option> + <option value="RF"><--- ---> (e.g. Solexa/Illumina mate-pair library)</option> + <option value="SB">2---> 1---> (e.g. Roche 454 paired-end libraries or IonTorrent long-mate; see note)</option> + </param> + <!-- min/max validation is done via the <code> tag --> + <param name="min_size" type="integer" optional="true" min="0" value="" + label="Minimum size of 'good' DNA templates in the library preparation" + help="Optional, but if used you must also supply a maximum value." /> + <param name="max_size" type="integer" optional="true" min="0" value="" + label="Maximum size of 'good' DNA templates in the library preparation" + help="Optional, but if used you must also supply a minimum value." /> + <param name="naming" type="select" label="Pair naming convention"> + <option value="solexa">Solexa/Illumina (using '/1' and '/2' suffixes, or later Illumina colon system)</option> + <option value="FR">Forward/Reverse scheme (using '.f*' and '.r*' suffixes)</option> + <option value="tigr">TIGR scheme (using 'TF*' and 'TR*' suffixes)</option> + <option value="sanger">Sanger scheme (see notes)</option> + <option value="stlouis">St. Louis scheme (see notes)</option> + </param> + </when> + <when value="none" /><!-- no further questions --> + </conditional> + <param name="filenames" type="data" format="fastq,mira" multiple="true" required="true" label="Read file(s)" + help="Multiple files allowed, for example paired reads can be given as two files (MIRA looks at read names to identify pairs)." /> + </repeat> + <param name="maf_wanted" type="boolean" label="Output assembly in MIRA's own format?" checked="False" /> + <param name="bam_wanted" type="boolean" label="Convert assembly into BAM format?" checked="True" /> + </inputs> + <outputs> + <data name="out_fasta" format="fasta" label="MIRA de novo contigs (FASTA)" /> + <data name="out_bam" format="bam" label="MIRA de novo assembly (BAM)"> + <filter>bam_wanted is True</filter> + </data> + <data name="out_maf" format="mira" label="MIRA de novo assembly"> + <filter>maf_wanted is True</filter> + </data> + <!-- TODO? + <data name="out_contigstats" format="tabular" label="MIRA contig stats" /> + --> + <data name="out_log" format="txt" label="MIRA de novo log" /> + </outputs> + <tests> + <!-- Tiger mitochondria, selected paired end Illumina reads from SRR639755 + Note we're using just one repeat group, and only the filenames parameter + within it, so this should work with current test framework limitations: + TODO: Revise example and/or -NW:cac=warn and -NW:acv=80 settings + MIRA 4.0 complains as coverage is about x93 which is over 80 limit. + Also MIRA 4.0 gives three contigs as output. + <test> + <param name="job_type" value="genome" /> + <param name="job_quality" value="accurate" /> + <param name="filenames" value="SRR639755_mito_pairs.fastq.gz" ftype="fastqsanger" /> + <output name="out_fasta" file="SRR639755_mito_pairs.mira4_de_novo.fasta" ftype="fasta" /> + </test> + --> + <!-- Simple assembly based on MIRA's minidemo/demo4 example + Note we're using just one repeat group, + but several parameters with the repeat + --> + <test> + <param name="job_type" value="genome" /> + <param name="job_quality" value="accurate" /> + <param name="technology" value="sanger" /> + <param name="type" value="none" /> + <param name="filenames" value="U13small_m.fastq" ftype="fastqsanger" /> + <param name="maf_wanted" value="true"/> + <param name="bam_wanted" value="true"/> + <output name="out_fasta" file="U13small_m.mira4_de_novo.fasta" ftype="fasta" /> + <output name="out_bam" file="empty_file.dat" compare="contains" /> + <!-- TODO: Suggest startswith as a compare method? --> + <output name="out_maf" file="header.mira" compare="contains" /> + <output name="out_log" file="empty_file.dat" compare="contains" /> + </test> + <!-- Simple assembly based on MIRA's minidemo/solexa1 example + Note we're using just one repeat group, + but two parameters within the repeat (filename, no pairing) + --> + <test> + <param name="job_type" value="genome" /> + <param name="job_quality" value="accurate" /> + <param name="type" value="none" /> + <param name="filenames" value="ecoli.fastq" ftype="fastqsanger" /> + <param name="maf_wanted" value="false"/> + <param name="bam_wanted" value="false"/> + <output name="out_fasta" file="ecoli.mira4_de_novo.fasta" ftype="fasta" /> + <output name="out_log" file="empty_file.dat" compare="contains" /> + </test> + </tests> + <help> + +**What it does** + +Runs MIRA v4.0 in de novo mode, collects the output, generates a sorted BAM +file, and then 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, Ion Torrent +and also PacBio). + +It is particularly suited to small genomes such as bacteria. + + +**Notes on paired reads** + +.. class:: warningmark + +MIRA uses read naming conventions to identify paired read partners +(and does not care about their order in the input files). In most cases, +the Solexa/Illumina setting is fine. For Sanger capillary sequencing, +you may need to rename your reads to match one of the standard conventions +supported by MIRA. For Roche 454 or Ion Torrent the appropriate settings +depend on how the FASTQ file was produced: + +* If using Roche's ``sffinfo`` or older versions of ``sff_extract`` + to convert SFF files to FASTQ, your reads will probably have the + ``---> <---`` orientation and use the ``.f`` and ``.r`` + suffixes (FR naming). + +* If using a recent version of ``sff_extract``, then the ``/1`` and ``/2`` + suffixes are used (Solexa/Illumina style naming) and the original + ``2---> 1--->`` orientation is preserved. + +The reason for this is the raw data for Roche 454 and Ion Torrent paired-end +libraries sequences a circularised fragment such that the raw data begins +with the end of the fragment, a linker, then the start of the fragment. +This means both the start and end are sequenced from the same strand, and +have the orientation ``2---> 1--->``. However, in order to use the data +with traditional tools expecting Sanger capillary style ``---> <---`` +orientation it was common to reverse complement one of the pair to mimic this. + + +**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/mira4_assembler + </help> + <citations> + <citation type="doi">10.7717/peerj.167</citation> + <citation type="bibtex">@ARTICLE{Chevreux1999-mira3, + author = {B. Chevreux and T. Wetter and S. Suhai}, + year = {1999}, + title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information}, + journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)} + volume = {99}, + pages = {45-56}, + url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html} + }</citation> + </citations> +</tool>