Mercurial > repos > crs4 > sequel
comparison sequel_wrapper.xml @ 1:ccadfae70b02 draft
Use $GALAXY_SLOTS instead of $SEQUEL_SITE_OPTIONS. Depend on package_blat_35x1 . Add readme.rst . Update Orione citation.
author | crs4 |
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date | Wed, 05 Mar 2014 06:48:08 -0500 |
parents | 58e1eb37fddc |
children | 208ce57f9221 |
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0:58e1eb37fddc | 1:ccadfae70b02 |
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4 <requirement type="package" version="0.6.2">bwa</requirement> | 4 <requirement type="package" version="0.6.2">bwa</requirement> |
5 <requirement type="package" version="35">blat</requirement> | 5 <requirement type="package" version="35">blat</requirement> |
6 <requirement type="package" version="1.0.2">sequel</requirement> | 6 <requirement type="package" version="1.0.2">sequel</requirement> |
7 </requirements> | 7 </requirements> |
8 <command interpreter="python"> | 8 <command interpreter="python"> |
9 sequel_wrapper.py | 9 sequel_wrapper.py -t \${GALAXY_SLOTS:-8} -p \${GALAXY_SLOTS:-8} -u 1 |
10 \${SEQUEL_SITE_OPTIONS:--t 8 -p 8 -u 1} | |
11 --sequel_jar_path=\$SEQUEL_JAR_PATH --read1=$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/ |