# 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
+
+