| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/big-tiandm/mirplant2/micrornas_v1/1.0.0 (this tool) |
| micrornas_v1 |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| fastx_toolkit | 0.0.13 | package |
| bowtie | 0.12.7 | package |
| SCRIPT_PATH | not provided | set_environment |
| SVG | 2.59 | package |
| ViennaRNA | 2.1.8 | package |
| Additional information about this tool |
microRNA.pl
## Change this to accommodate the number of threads you have available.
-t \${GALAXY_SLOTS:-4}
-path \$SCRIPT_PATH
## Do or not annotate known microRNAs
#if $params.known_microRNA == "yes":
-pre $pre -mat $mat
#end if
## prepare bowtie index
#set index_path = ''
#if str($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
-gfa ${index_path}.fa -idx $index_path -mis $mismatch -i $config -fa $reads -e $e -f $f -r $r -dis $dis -flank $flank -mfe $mfe > run.log
| Functional tests |