# HG changeset patch # User anmoljh # Date 1440692627 14400 # Node ID 972c930ed2784c1df01ec266f00ad6e0af366622 Uploaded diff -r 000000000000 -r 972c930ed278 align_and_estimate_abundance.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/align_and_estimate_abundance.xml Thu Aug 27 12:23:47 2015 -0400 @@ -0,0 +1,63 @@ + + + using utility align_and_estimate_abundance.pl + + + trinityrnaseq + bowtie + samtools + eXpress + + + \$TRINITY_HOME/util/align_and_estimate_abundance.pl + --transcripts $transcripts + --est_method $est_method + --aln_method $aln_method + --prep_reference + + ## Inputs. + #if str($reads.paired_or_single) == "paired": + + --left $reads.left_input --right $reads.right_input + + #if $reads.left_input.ext == 'fa': + --seqType fa + #else: + --seqType fq + #end if + + ## Additional parameters. + #if str($reads.optional.use_options) == "yes": + + #if str($reads.optional.library_type) != "None": + --SS_lib_type $reads.optional.library_type + #end if + + + + #end if + + #else: + --single $reads.input + + #if str($reads.input.ext) == 'fa': + --seqType fa + #else: + --seqType fq + #end if + + ## Additional parameters. + #if str($reads.optional.use_option) == "yes": + + #if str($reads.additional_params.library_type) != "None": + --SS_lib_type $reads.optional.library_type + #end if + + #end if + #end if + +## direct to output +> $align_and_estimate_abundance_log 2>&1 + + + diff -r 000000000000 -r 972c930ed278 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Aug 27 12:23:47 2015 -0400 @@ -0,0 +1,15 @@ + + + + + + + + + + + + + + +