Repository revision
4:8e96d712a2bd

Repository 'tetoolkit_tetranscripts'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/tetoolkit_tetranscripts

TEtranscripts tool metadata
Miscellaneous
annotates reads to genes and transposable elements
tetoolkit_tetranscripts
toolshed.g2.bx.psu.edu/repos/iuc/tetoolkit_tetranscripts/tetoolkit_tetranscripts/2.2.3+galaxy0
2.2.3+galaxy0
TEtranscripts --version
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/tetoolkit_tetranscripts/tetoolkit_tetranscripts/2.2.3+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/tetoolkit_tetranscripts/tetoolkit_tetranscripts/2.2.1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/tetoolkit_tetranscripts/tetoolkit_tetranscripts/2.2.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/tetoolkit_tetranscripts/tetoolkit_tetranscripts/2.1.4+galaxy0
tetoolkit_tetranscripts
Requirements (dependencies defined in the <requirements> tag set)
name version type
tetranscripts 2.2.3 package
Additional information about this tool
## initialize
## file extension is required
ln -s '$GTF' 'gene_annotation.gtf' &&
ln -s '$TE' 'transposable_annotation.gtf' &&

## run
TEtranscripts
## required
-t
#for $s in $sample_rep
    '${s.t}'
#end for
-c
#for $s in $sample_rep
    '${s.c}'
#end for
--GTF 'gene_annotation.gtf'
--TE 'transposable_annotation.gtf'
## optional
--stranded '$io.stranded'
$io.sortByPos
--project 'result'
--mode '$ap.mode'
--minread $ap.minread
#if $ap.fragmentLength
    --fragmentLength $ap.fragmentLength
#end if
--iteration $ap.iteration
--padj $ap.padj
--foldchange $ap.foldchange
#if 'log' in $oo.out
    --verbose 3
    |& tee '$out_log'
#end if
        
None
False
Functional tests
name inputs outputs required files
Test-1 sample_rep_0|t: treatment1.bam
sample_rep_0|c: control1.bam
sample_rep_1|t: treatment2.bam
sample_rep_1|c: control2.bam
GTF: gtf.gtf
TE: te.gtf
name: value
name: value
name: value
treatment1.bam
control1.bam
treatment2.bam
control2.bam
gtf.gtf
te.gtf
value
Test-2 sample_rep_0|t: treatment1.bam
sample_rep_0|c: control1.bam
sample_rep_1|t: treatment2.bam
sample_rep_1|c: control2.bam
GTF: gtf.gtf
TE: te.gtf
io|stranded: forward
io|sortByPos: True
ap|mode: uniq
ap|minread: 2
ap|fragmentLength: 10
ap|iteration: 90
ap|padj: 0.06
ap|foldchange: 2.0
oo|out: ['cnttable', 'deseq2', 'gta', 'sgt', 'log']
name: value
name: value
name: value
name: value
name: value
treatment1.bam
control1.bam
treatment2.bam
control2.bam
gtf.gtf
te.gtf
value
Test-3 sample_rep_0|t: treatment1.bam
sample_rep_0|c: control1.bam
sample_rep_1|t: treatment2.bam
sample_rep_1|c: control2.bam
GTF: gtf.gtf
TE: te.gtf
io|stranded: reverse
oo|out: ['cnttable', 'deseq2', 'gta', 'sgt', 'log']
name: value
name: value
name: value
name: value
name: value
treatment1.bam
control1.bam
treatment2.bam
control2.bam
gtf.gtf
te.gtf
value