# HG changeset patch
# User rogerngo
# Date 1337142216 14400
# Node ID f8037d6c5f14c46a0777d29e45791526cdc565d4
# Parent  e21466396cc8ec0fdd451797415daed1e30e752d
Galaxy XML

diff -r e21466396cc8 -r f8037d6c5f14 iAssembler.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/iAssembler.xml	Wed May 16 00:23:36 2012 -0400
@@ -0,0 +1,28 @@
+<tool id="iAssembler" name="iAssembler" version="1.3">
+	<description>Assembly of transcriptomes.</description>
+	<requirements>
+		<requirement type="package">iAssembler</requirement>
+	</requirements>
+	<command interpreter="perl">
+		iAssembler_wrapper.pl -i $input -e $maxlength -h $minoverlap -p $minpercent
+	</command>
+	<inputs>
+	<param name="input" format="fasta" type="data" label="nucleotide fasta file"/>
+	<param name="maxlength" type="integer" value="30" label="maximum length of end clips (6~100; default = 30)"/>
+	<param name="minoverlap" type="integer" value="40" label="minimum overlap length (>=30; default = 40)"/>
+	<param name="minpercent" type="integer" value="97" label="minimum percent identity for sequence clustering and assembly (95~100; default = 97)"/>
+	</inputs>
+	<outputs>
+		<data format="fasta" name="Assembled" from_work_dir="unigene_seq.fasta"/>
+	</outputs>
+	<tests>
+	</tests>
+	<help>
+	iAssembler is a standalone package to assemble ESTs generated using Sanger and/or Roche-454 pyrosequencing technologies into contigs. The pipeline gives much higher accuracy in EST assembly than other existing assemblers by employing an iterative assembly strategy and automated error corrections of mis-assemblies. iAssembler first performs iterative assemblies using MIRA and CAP3 (default: four cycles of MIRA assemblies followed by one CAP3 assembly) to correct assembly errors (mostly sequences derived from the same transcript fail to be assembled together) which occur frequently in just one round of assembly. The program then performs post-assembly quality checking by 1) aligning each EST sequence to its corresponding unigene sequence to identify mis-assemblies; and 2) performing all-verus-all pair-wise sequence alignments of unigenes to identify sequences derived from same transcripts that fail to be assembled together. The identified mis-assemblies are then corrected by the program automatically.
+
+http://bioinfo.bti.cornell.edu/tool/iAssembler/
+
+Citation:
+Zheng Y, Zhao L, Gao J, Fei Z. (2011) iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences. BMC Bioinformatics 12:453
+	</help>
+</tool>