Mercurial > repos > peterjc > mira_assembler
changeset 6:1e49ca6731cd draft
Uploaded v0.0.7 take 4, declare package dependency in main tool XML.
| author | peterjc |
|---|---|
| date | Wed, 24 Apr 2013 12:54:44 -0400 |
| parents | c6bbce601b69 |
| children | e810e45bdad7 |
| files | tools/mira_3_4/mira.xml |
| diffstat | 1 files changed, 21 insertions(+), 20 deletions(-) [+] |
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--- a/tools/mira_3_4/mira.xml Wed Apr 24 12:49:41 2013 -0400 +++ b/tools/mira_3_4/mira.xml Wed Apr 24 12:54:44 2013 -0400 @@ -1,7 +1,12 @@ <tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6"> <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> @@ -124,22 +129,18 @@ <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> + </tests> + <help> **What it does** @@ -151,5 +152,5 @@ 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> + </help> </tool>