| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/fargene/fargene/0.1+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/fargene/fargene/0.1 |
| fargene |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| fargene | 0.1 | package |
| tar | 1.32 | package |
| Additional information about this tool |
#import re
#if $inputs.input_type == 'paired':
#set $safename_R1 = re.sub('[^\w\-_\.]', '_', $inputs.R1.element_identifier)
#set $safename_R2 = re.sub('[^\w\-_\.]', '_', $inputs.R2.element_identifier)
ln -fs '$inputs.R1' ${safename_R1}.fastq &&
ln -fs '$inputs.R2' ${safename_R2}.fastq &&
#elif $inputs.input_type == 'collection':
#for $i, $input in enumerate($inputs.input_collection)
#set $safename_fwd = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
ln -fs '${input.forward}' ${safename_fwd}_1.fastq &&
#set $safename_rvs = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
ln -fs '${input.reverse}' ${safename_rvs}_2.fastq &&
#end for
#elif $inputs.input_type == 'sequence':
#for $input in $inputs.input_sequence
#set $safename_seq = re.sub('[^\w\-_\.]', '_', $input.element_identifier)
ln -fs '$input' ${safename_seq}.fasta &&
#end for
#end if
fargene
--infiles
#if $inputs.input_type in ('paired', 'collection'):
*.fastq
--meta
#elif $inputs.input_type == 'sequence':
*.fasta
#end if
--hmm-model $models
--output fargene_output
--tmp-dir tmp
-p \${GALAXY_SLOTS:-4}
#if $meta_score != 0.0:
--meta-score '$meta_score'
#end if
#if $score != 0.0:
--score '$score'
#end if
#if $protein:
'$protein'
#end if
#if $min_orf_length != 90:
--min-orf-length '$min_orf_length'
#end if
#if $retrieve_whole:
'$retrieve_whole'
#end if
#if $no_orf_predict:
'$no_orf_predict'
#end if
#if $no_quality_filtering:
'$no_quality_filtering'
#end if
#if $no_assembly:
'$no_assembly'
#end if
#if $orf_finder:
'$orf_finder'
#end if
#if $store_peptides:
'$store_peptides'
#end if
&&
#if $inputs.input_type in ('paired', 'collection'):
tar -czf retrievedFragments.tar.gz fargene_output/retrievedFragments
#end if
2>&1
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
inputs|R1: reads_1.fastq inputs|R2: reads_2.fastq inputs|input_type: paired |
name: value |
reads_1.fastq reads_2.fastq value |
| Test-2 |
inputs|input_collection: list:paired collection inputs|input_type: collection |
name: value |
reads_1.fastq reads_2.fastq value |
| Test-3 |
inputs|input_sequence: klebsiella_plasmid.fasta inputs|input_type: sequence |
name: value |
klebsiella_plasmid.fasta value |