| Miscellaneous |
| Version lineage of this tool (guids ordered most recent to oldest) |
| toolshed.g2.bx.psu.edu/repos/iuc/flair_collapse/flair_collapse/1.5+galaxy1 (this tool) |
| toolshed.g2.bx.psu.edu/repos/iuc/flair_collapse/flair_collapse/1.5+galaxy0 |
| toolshed.g2.bx.psu.edu/repos/iuc/flair_collapse/flair_collapse/1.5 |
| flair_collapse |
| Requirements (dependencies defined in the <requirements> tag set) |
| name | version | type |
| flair | 1.5 | package |
| Additional information about this tool |
#if str($reference_source_genome.ref_selector_genome) == 'history':
#set reference = $reference_source_genome.reffile
#set ext = $reference.ext
samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for indexing fasta reference for flair" >&2 &&
#else
#set reference = $reference_source_genome.reffile.fields.path
#set ext = $reference_source_genome.reffile.fields.path
#end if
#if $ext.endswith(".gz"):
gunzip -c '$reference' > reference.fa &&
#else:
ln -sf '$reference' reference.fa &&
#end if
ln -s '$input_query' query.bed &&
flair.py collapse
###########
## Input ##
###########
-q query.bed
-r '$input_reads'
-g reference.fa
-f '$input_gtf'
#if $input_promotors:
-p '$input_promotors'
#end if
########################
## Additional Options ##
########################
-w $additional_options.window
-s $additional_options.support
$additional_options.stringent
#if str($additional_options.select_uniqueness):
-n str($additional_options.select_uniqueness)
#end if
$additional_options.isoform
--max_ends $additional_options.maxends
$additional_options.trustends
#if str($additional_options.select_filter):
-e str($additional_options.select_filter)
#end if
--quality $additional_options.mapq
#########
## END ##
#########
| Functional tests |
| name | inputs | outputs | required files |
| Test-1 |
input_query: flair_all_corrected.bed input_reads: chrM.fastq.gz reference_source_genome|reffile: chrM.fa reference_source_genome|ref_selector_genome: history input_gtf: UCSC_Main_on_Human_knownGene_region_chrM.gtf additional_outputs|out_format: ['bed', 'fasta'] |
name: value name: value name: value |
flair_all_corrected.bed chrM.fastq.gz chrM.fa UCSC_Main_on_Human_knownGene_region_chrM.gtf value |
| Test-2 |
input_query: flair_all_corrected.bed input_reads: chrM.fastq.gz reference_source_genome|reffile: chrM reference_source_genome|ref_selector_genome: cached input_gtf: UCSC_Main_on_Human_knownGene_region_chrM.gtf additional_outputs|out_format: ['bed', 'fasta'] |
name: value name: value name: value |
flair_all_corrected.bed chrM.fastq.gz UCSC_Main_on_Human_knownGene_region_chrM.gtf value |