Mercurial > repos > rnateam > antarna
changeset 5:01ca3429ae6c draft
Uploaded
author | rnateam |
---|---|
date | Tue, 12 May 2015 08:04:20 -0400 |
parents | d37265c1d1ad |
children | 3d00f7b51b9c |
files | antarna.xml |
diffstat | 1 files changed, 14 insertions(+), 26 deletions(-) [+] |
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line diff
--- a/antarna.xml Fri May 08 11:37:52 2015 -0400 +++ b/antarna.xml Tue May 12 08:04:20 2015 -0400 @@ -107,8 +107,8 @@ #if $Cseqw and $Cseqw is not None: -Cseqw $Cseqw #end if +$ov $v -$ov > $default]]></command> <inputs> <param label="Structure constraint using RNA dotbracket notation with fuzzy block constraint. (-Cstr)" name="Cstr" type="text"/> @@ -141,40 +141,28 @@ <param checked="false" label="Prints additional output to the headers of the produced sequences. (-ov)" name="ov" type="boolean" truevalue="-ov" falsevalue=""/> </inputs> <outputs> - <data format="fasta" name="default"/> + <data format="fasta" hidden="false" name="default"/> </outputs> - <tests> - <test> - <param name="Cstr" value="..((..)).."/> - <param name="tGC" value="0.5"/> - <param name="n" value="2"/> - <output name="default"> - <assert_contents> - <has_line_matching expression="[AGCT]{10}"/> - </assert_contents> - </output> - </test> - </tests> <help><![CDATA[ +. =========================== antaRNA - ant assembled RNA =========================== - - For antaRNA only the VIENNNA RNA Package must be installed on your linux system. - antaRNA will only check, if the executables of RNAfold and RNAdistance of the ViennaRNA package can be found. If those programs are - not installed correctly, no output will be generated, an also no warning will be prompted. - So the binary path of the Vienna Tools must be set up correctly in your system's PATH variable in order to run antaRNA correctly! - - - For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/ +- antaRNA uses the VIENNNA RNA Package + - specifically it uses RNAfold and RNAdistance to calculate energies of and distances between secondary structures (version 2.1.x) + - for the parametrization of antaRNA the version 2.1.3 of the ViennaRNA package was used - Example calls: - antaRNA --Cstr "...(((...)))..." --tGC 0.5 -n 2 - antaRNA --Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov - antaRNA --Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10 + +- For questions and remarks please feel free to contact us at http://www.bioinf.uni-freiburg.de/ + +Example calls: + antaRNA --Cstr "...(((...)))..." --tGC 0.5 -n 2 + antaRNA --Cstr ".........AAA(((...)))AAA........." --tGC 0.5 -n 10 --output_file /path/to/antaRNA_TESTRUN -ov + antaRNA --Cstr "BBBBB....AAA(((...)))AAA....BBBBB" --Cseq "NNNNANNNNNCNNNNNNNNNNNGNNNNNNUNNN" --tGC 0.5 -n 10 + ]]></help> -<citations> -</citations> </tool>