Mercurial > repos > bernhardlutz > exparna
changeset 1:51e200ccf18e draft
Uploaded
author | bernhardlutz |
---|---|
date | Sat, 28 Dec 2013 15:09:10 -0500 |
parents | 4699a84c41d8 |
children | 414f51a0b5b5 |
files | exparna.xml tool_dependencies.xml |
diffstat | 2 files changed, 14 insertions(+), 4 deletions(-) [+] |
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--- a/exparna.xml Mon Dec 23 18:02:44 2013 -0500 +++ b/exparna.xml Sat Dec 28 15:09:10 2013 -0500 @@ -7,8 +7,10 @@ <command> ExpaRNA -t$emp_scoring +#if $check == "no": +-n$max_used_sub +#end if -s$min_incl_sub --n$max_used_sub $locarna_input $alignment_to_file $list_in_file @@ -16,7 +18,7 @@ $fastafile; mkdir $outfile.files_path; cp ./ExpaRNA-results/* $outfile.files_path; - python /home/bernhard/galaxytools/rna_tools/exparna/create_html.py $outfile $outfile.files_path; + python \$EXPARNA_SCRIPT_PATH/create_html.py $outfile $outfile.files_path; </command> <stdio> <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" /> @@ -48,7 +50,8 @@ </outputs> <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. + +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** You will receive a zip file containing all output files
--- a/tool_dependencies.xml Mon Dec 23 18:02:44 2013 -0500 +++ b/tool_dependencies.xml Sat Dec 28 15:09:10 2013 -0500 @@ -13,10 +13,17 @@ </repository> </action> <action type="shell_command">./configure --prefix $INSTALL_DIR --with-RNA=$ROOT_VIENNA_RNA_DIR</action> - <action type="make_install" /> + <action type="make_install" /> + <action type="move_file"> + <source>create_html.py</source> + <destination>$INSTALL_DIR</destination> + </action> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> + <action type="set_environment"> + <environment_variable action="set" name="EXPARNA_SCRIPT_PATH">$INSTALL_DIR</environment_variable> + </action> </actions> </install> <readme>Compiling ExpaRNA requires a C compiler (typically gcc)</readme>