Mercurial > repos > peterjc > mira_assembler
diff tools/mira_3_4/mira.xml @ 9:5573d802e431 draft
Uploaded v0.0.8, MIT licence, RST for README, citation information, development moved to GitHub.
| author | peterjc |
|---|---|
| date | Wed, 18 Sep 2013 06:22:19 -0400 |
| parents | 4266cccbb45a |
| children |
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--- a/tools/mira_3_4/mira.xml Wed Apr 24 12:43:17 2013 -0400 +++ b/tools/mira_3_4/mira.xml Wed Sep 18 06:22:19 2013 -0400 @@ -1,7 +1,12 @@ -<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6"> +<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8"> <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> - <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 + <requirements> + <requirement type="python-module">Bio</requirement> + <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 @@ -52,7 +57,7 @@ -DI:trt=/tmp </command> - <inputs> + <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> @@ -124,32 +129,63 @@ <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> - </tests> - <requirements> - <requirement type="python-module">Bio</requirement> - <requirement type="binary">mira</requirement> - </requirements> - <help> + </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 tool in scientific work leading to a publication, please cite: +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 -Chevreux et al. (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. +Chevreux et al. (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. - </help> +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>