Mercurial > repos > dereeper > mafft
diff mafft.xml @ 0:d7a735d3625e draft default tip
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| author | dereeper |
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| date | Wed, 17 Oct 2012 09:12:24 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mafft.xml Wed Oct 17 09:12:24 2012 -0400 @@ -0,0 +1,137 @@ +<tool id="mafft1" name="MAFFT"> + <description>, a progressive multiple alignment builder</description> + <command interpreter="bash">./mafft --quiet +#if $datatype_condition.type == "nt": + --nuc +#end if +#if $datatype_condition.type == "aa": + --amino +#end if +#if $datatype_condition.type != "nt": + #if $datatype_condition.PAM_value_condition.matrix == "bl30": + --bl 30 + #end if + #if $datatype_condition.PAM_value_condition.matrix == "bl45": + --bl 45 + #end if + #if $datatype_condition.PAM_value_condition.matrix == "bl62": + --bl 62 + #end if + #if $datatype_condition.PAM_value_condition.matrix == "bl80": + --bl 80 + #end if + #if $datatype_condition.PAM_value_condition.matrix == "PAM": + --jtt $datatype_condition.PAM_value_condition.PAM_value + #end if +#end if + --maxiterate $iterations --$distance_method --op $op --ep $ep $input > $output</command> + <inputs> + <param format="txt" name="input" type="data" label="Source file"/> + <conditional name="datatype_condition"> + <param type="select" name="type" label="Data type"> + <option value="auto">Automatic detection</option> + <option value="nt">Nucleic acids</option> + <option value="aa">Amino acids</option> + </param> + <when value="aa"> + <conditional name="PAM_value_condition"> + <param type="select" name="matrix" label="Matrix" help="Usefull only for amino acids"> + <option value="bl62">BLOSUM 62</option> + <option value="bl30">BLOSUM 30</option> + <option value="bl45">BLOSUM 45</option> + <option value="bl80">BLOSUM 80</option> + <option value="PAM">PAM</option> + </param> + <when value="bl30"></when> + <when value="bl45"></when> + <when value="bl62"></when> + <when value="bl80"></when> + <when value="PAM"> + <param type="text" name="PAM_value" help="Must be greater than 0" value="80" label="Coefficient of the PAM matrix" /> + </when> + </conditional> + </when> + <when value="auto"> + <conditional name="PAM_value_condition"> + <param type="select" name="matrix" label="Matrix" help="Usefull only for amino acids"> + <option value="bl62">BLOSUM 62</option> + <option value="bl30">BLOSUM 30</option> + <option value="bl45">BLOSUM 45</option> + <option value="bl80">BLOSUM 80</option> + <option value="PAM">PAM</option> + </param> + <when value="bl30"></when> + <when value="bl45"></when> + <when value="bl62"></when> + <when value="bl80"></when> + <when value="PAM"> + <param type="text" name="PAM_value" help="Must be greater than 0" value="80" label="Coefficient of the PAM matrix" /> + </when> + </conditional> + </when> + <when value="nt"> + </when> + </conditional> + <param type="text" name="iterations" help="1000 for maximum quality" value="1000" label="Maximum number of iterations" /> + <param type="text" name="op" help="1.53 default value" value="1.53" label="Gap opening penalty" /> + <param type="text" name="ep" help="0.0 default value" value="0.0" label="Gap extension penalty" /> + <param type="select" name="distance_method" label="Distance method" help="Distance method must be chosen regarding your data"> + <option value="6merpair">Shared 6mers distance (fastest)</option> + <option value="globalpair">Global alignment (NW)</option> + <option value="localpair">Local alignment (SW)</option> + <option value="genafpair">Local, affine gap cost</option> + <option value="fastapair">FASTA distance</option> + </param> + </inputs> + <outputs> + <data format="fasta" name="output" /> + </outputs> + <help> + +.. class:: infomark + +**Program encapsulated in Galaxy by Southgreen** + + +.. class:: infomark + +**MAFFT version 6.717b, 2009** + +----- + +============== + Please cite: +============== + +"Parallelization of the MAFFT multiple sequence alignment program.", **Katoh, Toh**, Bioinformatics 26:1899-1900, 2010. (describes the multithread version; Linux only) + +"Multiple Alignment of DNA Sequences with MAFFT.", **Katoh, Asimenos, Toh**, Methods in Molecular Biology 537:39-64, 2009. (outlines DNA alignment methods and several tips including group-to-group alignment and rough clustering of a large number of sequences) + +"Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework.", **Katoh, Toh**, BMC Bioinformatics 9:212, 2008. (describes RNA structural alignment methods) + +"Recent developments in the MAFFT multiple sequence alignment program.", **Katoh, Toh**, Briefings in Bioinformatics 9:286-298, 2008. (outlines version 6; Fast Breaking Paper in Thomson Reuters' ScienceWatch) + +"PartTree: an algorithm to build an approximate tree from a large number of unaligned sequences." **Katoh, Toh**, Bioinformatics 23:372-374, Errata, 2007. (describes the PartTree algorithm) + +"MAFFT version 5: improvement in accuracy of multiple sequence alignment.", **Katoh, Kuma, Toh, Miyata**, Nucleic Acids Res. 33:511-518, 2005. (describes [ancestral versions of] the G-INS-i, L-INS-i and E-INS-i strategies) + +"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform.", **Katoh, Misawa, Kuma, Miyata**, Nucleic Acids Res. 30:3059-3066, 2002. + + +----- + +========== + Overview +========== + +MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i wich is accurate for alignment with less than 200 sequences, FFT-NS-2 which is fast for alignment with less than 10000 sequences. + +----- + +For further informations, please visite the MAFFT_ website. + +.. _MAFFT: http://mafft.cbrc.jp/alignment/software/ + + </help> + +</tool> \ No newline at end of file