# HG changeset patch # User anmoljh # Date 1440681673 14400 # Node ID 9d038c34fe16331c42a520134ef75081e193c7ab Uploaded diff -r 000000000000 -r 9d038c34fe16 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Aug 27 09:21:13 2015 -0400 @@ -0,0 +1,6 @@ + + + + + + diff -r 000000000000 -r 9d038c34fe16 trinity.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/trinity.xml Thu Aug 27 09:21:13 2015 -0400 @@ -0,0 +1,129 @@ + + + + + + De novo assembly of RNA-Seq data Using Trinity + + trinityrnaseq + + + Trinity --JM $JM --CPU $CPU + + ## Inputs. + #if str($inputs.paired_or_single) == "paired": + --left $inputs.left_input --right $inputs.right_input + #if $inputs.left_input.ext == 'fa': + --seqType fa + #else: + --seqType fq + #end if + #if str($inputs.library_type) != "None": + --SS_lib_type $inputs.library_type + #end if +--group_pairs_distance $inputs.group_pairs_distance + #else: + --single $inputs.input + #if str($inputs.input.ext) == 'fa': + --seqType fa + #else: + --seqType fq + #end if + #if str($inputs.library_type) != "None": + --SS_lib_type $inputs.library_type + #end if + #end if + + ## Additional parameters. + #if str($additional_params.use_additional) == "yes": +--min_kmer_cov $inputs.min_kmer_cov --max_reads_per_graph $inputs.max_reads_per_graph --bflyHeapSpaceMax $input.bflyHeapSpaceMax +#if $inputs.bfly_opts != 'None': +--bfly_opts " $inputs.bfly_opts " +#end if + #end if + + + ## direct to output + > $trinity_log 2>&1 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Trinity is a de novo transcript assembler that uses RNA-seq data as input. This tool runs all Trinity_ commands--Inchworm, Chrysalis, and Butterfly--in a single pass. + + .. _Trinity: http://trinityrnaseq.sourceforge.net + +