Mercurial > repos > crs4 > sequel
diff sequel_wrapper.xml @ 1:ccadfae70b02 draft
Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation.
| author | crs4 |
|---|---|
| date | Wed, 05 Mar 2014 06:48:08 -0500 |
| parents | 58e1eb37fddc |
| children | 208ce57f9221 |
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--- a/sequel_wrapper.xml Tue Oct 15 11:15:28 2013 -0400 +++ b/sequel_wrapper.xml Wed Mar 05 06:48:08 2014 -0500 @@ -6,8 +6,7 @@ <requirement type="package" version="1.0.2">sequel</requirement> </requirements> <command interpreter="python"> - sequel_wrapper.py - \${SEQUEL_SITE_OPTIONS:--t 8 -p 8 -u 1} + sequel_wrapper.py -t \${GALAXY_SLOTS:-8} -p \${GALAXY_SLOTS:-8} -u 1 --sequel_jar_path=\$SEQUEL_JAR_PATH --read1=$read1 --read2=$read2 --contigs=$contigs #if str($bases_length) --bases_length=$bases_length @@ -78,11 +77,11 @@ <param name="min_aln_score" type="integer" value="1" optional="true" label="Min alignment score (MAPQ) of reads to consider (-q)" help="" /> - <param name="single_cell_mode" type="boolean" optional="true" checked="false" label="Single cell mode, sort partial-contigs by coverage (-s)" /> + <param name="single_cell_mode" type="boolean" checked="false" label="Single cell mode, sort partial-contigs by coverage (-s)" /> - <param name="report_changes" type="boolean" optional="true" checked="false" label="Report changes (slow) for all input-contigs (-r)" /> + <param name="report_changes" type="boolean" checked="false" label="Report changes (slow) for all input-contigs (-r)" /> - <param name="extend_contig" type="boolean" optional="true" checked="false" label="Extend contig with flanking regions of alignment (-e)" /> + <param name="extend_contig" type="boolean" checked="false" label="Extend contig with flanking regions of alignment (-e)" /> <param name="reference_genome" type="data" format="fasta,twobit" optional="true" label="Evaluate refinement using reference genome (-g)" help="FASTA or 2bit format" /> </inputs> @@ -120,7 +119,7 @@ If you use this tool in Galaxy, please cite |Cuccuru2013|_. -.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2013) Orione, a web-based framework for NGS analysis in microbiology. *Submitted* +.. |Cuccuru2013| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted .. _Cuccuru2013: http://orione.crs4.it/ This tool uses `SEQuel`_, which is licensed separately. Please cite |Ronen2012|_.