Mercurial > repos > bernhardlutz > exparna
changeset 6:683f4c13662d draft default tip
Uploaded
author | bernhardlutz |
---|---|
date | Thu, 09 Jan 2014 14:11:19 -0500 |
parents | b75c2fe4cf88 |
children | |
files | exparna.xml |
diffstat | 1 files changed, 18 insertions(+), 2 deletions(-) [+] |
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--- a/exparna.xml Thu Jan 09 12:54:13 2014 -0500 +++ b/exparna.xml Thu Jan 09 14:11:19 2014 -0500 @@ -19,6 +19,9 @@ mkdir $outfile.files_path; cp ./ExpaRNA-results/* $outfile.files_path; python \$EXPARNA_SCRIPT_PATH/create_html.py $outfile $outfile.files_path; +#if $locarna_input: + cp ./ExpaRNA-results/LCSEPM_LocARNA_* $locarna_inputfile +#end if </command> <stdio> <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> @@ -46,14 +49,27 @@ <param name="all_in_file" type="boolean" checked="false" truevalue="-a" falsevalue="" label="Write all EPMs into file" help="-a" /> </inputs> <outputs> + <data format="fasta" name="locarna_inputfile" label="Output generated for Locarna"> + <filter>locarna_input is True</filter> + </data> <data name="outfile" format="zip" /> </outputs> + <tests> + <test> + <param name="fastafile" value="input.fasta" /> + <output name="output" file="output.zip" compare="sim_size" /> + <param name="locarna_input" value="" /> + <param name="check_all" value="yes" /> + </test> + + </tests> <help>**What it does** http://rna.informatik.uni-freiburg.de/ExpaRNA/Input.jsp ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Instead of computing a full sequence-structure alignment, it computes the best arrangement of sequence-structure motifs common to two RNAs. A motif is a local (or isolated) substructure which is identical to both RNAs. ExpaRNA requires a given nested secondary structure for both RNAs. If no structure is available, RNAfold from Vienna RNA Package is used for a structure prediction. The accuracy of the algorithm is mainly controlled by the minimal size of the included sequence-structure motifs. ExpaRNA is especially useful for comparative structural RNA analysis and to speed-up complex sequence-structure alignment methods. For this purpose, the predicted common substructures by ExpaRNA are used as anchor constraints for a full structural alignment. + +**Output** - **Output** - You will receive a zip file containing all output files +You will receive a zip file containing all output files and optionally the outputfile made for postprocessing with locarna. </help> </tool>