Miscellaneous |
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
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 |