| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/big-tiandm/mirplant2/plant_sirna_v1/1.0.0 (this tool) |
| plant_sirna_v1 |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| SCRIPT_PATH | not provided | set_environment |
| bowtie | 0.12.7 | package |
| R | 3.0.1 | package |
| fastx_toolkit | 0.0.13 | package |
| threads | 1.96 | package |
| Parallel-ForkManager | 1.06 | package |
| SVG | 2.59 | package |
| Boost-Graph | 1.4_001 | package |
| Additional information about this tool |
siRNA_pipeline.pl
## Change this to accommodate the number of threads you have available.
-t \${GALAXY_SLOTS:-4}
-path \$SCRIPT_PATH
## prepare bowtie index
#set index_path = ''
#if str($reference_genome.source) == "history":
bowtie-build "$reference_genome.own_file" genome; ln -s "$reference_genome.own_file" genome.fa;
#set index_path = 'genome'
#else:
#set index_path = $reference_genome.index.fields.path
#end if
## Do or not annotate siRNAs by function
#if $params.function_anno == "yes":
-nat $params.nat -repeat $params.repeat
#end if
## Do or not DEG
#if $degseq.degseq_analysis == "yes" :
-deg $degseq.deg
#end if
-i $reads -config $config -n $hits -format $format -g ${index_path}.fa -idx $index_path -f $gff -mis $mis -d $d -p $p -l $l -cen $cen -span $span > run.log
| Functional tests |