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comparison sequel_wrapper.xml @ 1:ccadfae70b02 draft

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Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation.
author crs4
date Wed, 05 Mar 2014 06:48:08 -0500
parents 58e1eb37fddc
children 208ce57f9221
comparison
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0:58e1eb37fddc 1:ccadfae70b02
4 <requirement type="package" version="0.6.2">bwa</requirement> 4 <requirement type="package" version="0.6.2">bwa</requirement>
5 <requirement type="package" version="35">blat</requirement> 5 <requirement type="package" version="35">blat</requirement>
6 <requirement type="package" version="1.0.2">sequel</requirement> 6 <requirement type="package" version="1.0.2">sequel</requirement>
7 </requirements> 7 </requirements>
8 <command interpreter="python"> 8 <command interpreter="python">
9 sequel_wrapper.py 9 sequel_wrapper.py -t \${GALAXY_SLOTS:-8} -p \${GALAXY_SLOTS:-8} -u 1
10 \${SEQUEL_SITE_OPTIONS:--t 8 -p 8 -u 1}
11 --sequel_jar_path=\$SEQUEL_JAR_PATH --read1=$read1 --read2=$read2 --contigs=$contigs 10 --sequel_jar_path=\$SEQUEL_JAR_PATH --read1=$read1 --read2=$read2 --contigs=$contigs
12 #if str($bases_length) 11 #if str($bases_length)
13 --bases_length=$bases_length 12 --bases_length=$bases_length
14 #end if 13 #end if
15 #if str($kmer_size) 14 #if str($kmer_size)
76 75
77 <param name="discard_positional" type="integer" value="1" optional="true" label="Discard positional k-mers observed less than n times (-n)" help="" /> 76 <param name="discard_positional" type="integer" value="1" optional="true" label="Discard positional k-mers observed less than n times (-n)" help="" />
78 77
79 <param name="min_aln_score" type="integer" value="1" optional="true" label="Min alignment score (MAPQ) of reads to consider (-q)" help="" /> 78 <param name="min_aln_score" type="integer" value="1" optional="true" label="Min alignment score (MAPQ) of reads to consider (-q)" help="" />
80 79
81 <param name="single_cell_mode" type="boolean" optional="true" checked="false" label="Single cell mode, sort partial-contigs by coverage (-s)" /> 80 <param name="single_cell_mode" type="boolean" checked="false" label="Single cell mode, sort partial-contigs by coverage (-s)" />
82 81
83 <param name="report_changes" type="boolean" optional="true" checked="false" label="Report changes (slow) for all input-contigs (-r)" /> 82 <param name="report_changes" type="boolean" checked="false" label="Report changes (slow) for all input-contigs (-r)" />
84 83
85 <param name="extend_contig" type="boolean" optional="true" checked="false" label="Extend contig with flanking regions of alignment (-e)" /> 84 <param name="extend_contig" type="boolean" checked="false" label="Extend contig with flanking regions of alignment (-e)" />
86 85
87 <param name="reference_genome" type="data" format="fasta,twobit" optional="true" label="Evaluate refinement using reference genome (-g)" help="FASTA or 2bit format" /> 86 <param name="reference_genome" type="data" format="fasta,twobit" optional="true" label="Evaluate refinement using reference genome (-g)" help="FASTA or 2bit format" />
88 </inputs> 87 </inputs>
89 88
90 <outputs> 89 <outputs>
118 .. _CRS4 Srl.: http://www.crs4.it/ 117 .. _CRS4 Srl.: http://www.crs4.it/
119 .. _MIT license: http://opensource.org/licenses/MIT 118 .. _MIT license: http://opensource.org/licenses/MIT
120 119
121 If you use this tool in Galaxy, please cite |Cuccuru2013|_. 120 If you use this tool in Galaxy, please cite |Cuccuru2013|_.
122 121
123 .. |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* 122 .. |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
124 .. _Cuccuru2013: http://orione.crs4.it/ 123 .. _Cuccuru2013: http://orione.crs4.it/
125 124
126 This tool uses `SEQuel`_, which is licensed separately. Please cite |Ronen2012|_. 125 This tool uses `SEQuel`_, which is licensed separately. Please cite |Ronen2012|_.
127 126
128 .. _SEQuel: http://bix.ucsd.edu/SEQuel/ 127 .. _SEQuel: http://bix.ucsd.edu/SEQuel/