Mercurial > repos > galaxyp > nbic_fasta
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| author | galaxyp |
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| date | Fri, 10 May 2013 17:15:08 -0400 |
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<!-- # ===================================================== # $Id: GenerateDegenerateFasta.xml 90 2011-01-19 13:20:31Z pieter.neerincx@gmail.com $ # $URL: https://trac.nbic.nl/svn/galaxytools/trunk/tools/general/FastaTools/GenerateDegenerateFasta.xml $ # $LastChangedDate: 2011-01-19 07:20:31 -0600 (Wed, 19 Jan 2011) $ # $LastChangedRevision: 90 $ # $LastChangedBy: pieter.neerincx@gmail.com $ # ===================================================== --> <tool id="GenerateDegenerateFasta1" name="GenerateDegenerateFasta" version="2.1"> <description>Creates a FASTA file with all possible sequences for degenerate sequences.</description> <command interpreter="perl"> #if $sequence_features.acid_type=="aa" #GenerateDegenerateFasta.pl -i $input -p $pcol -s $scol -t aa -o $output -x $sequence_features.xexpansion -l WARN #elif $sequence_features.acid_type=="dna" #GenerateDegenerateFasta.pl -i $input -p $pcol -s $scol -t dna -o $output -l WARN #elif $sequence_features.acid_type=="rna" #GenerateDegenerateFasta.pl -i $input -p $pcol -s $scol -t rna -o $output -l WARN #end if </command> <inputs> <param format="tabular" name="input" type="data" label="Degenerate sequences" help="(in tab delimited format)"/> <param name="pcol" type="data_column" value="1" data_ref="input" label="Prefix column" help="Prefixes will be used as the first part of unique identifiers for the generated sequences."/> <param name="scol" type="data_column" value="2" data_ref="input" label="Sequence column"/> <conditional name='sequence_features'> <param name="acid_type" type="select" accept_default="true" mmultiple="false" label="The degenerate sequences represent"> <label>The degenerate sequences represent</label> <option value="aa">Proteins</option> <option value="dna">DNA</option> <option value="rna">RNA</option> </param> <when value="aa"> <param name="xexpansion" type="select" accept_default="true" mmultiple="false" label="The degenerate amino acid X represents"> <label>The degenerate amino acid X represents</label> <option value="20">The 20 most common amino acids</option> <option value="22">All 22 amino acids</option> </param> </when> <when value="dna"> </when> <when value="rna"> </when> </conditional> </inputs> <outputs> <data format="fasta" name="output" label="FASTA sequences for ${input.name}"/> </outputs> <!-- <tests> <test> <param name="input" value="GenerateDegenerateFasta_example_input.txt"/> <output name="output" file="GenerateDegenerateFasta_example_output.fasta" ftype="fasta"/> </test> </tests> --> <help> .. class:: infomark **What it does** This tool creates a multi-sequence FASTA file with all possible sequences based on degenerate input sequences. The input must be a tab delimited file containing at least 2 columns. One with the degenerate sequences and the other with a prefix that will be used to give each of generated sequences a unique identifier. In addition to the prefix, the generated identifiers will contain an underscore followed by an incremented number. =================================================== *Degenerate (wild card) amino acids* =================================================== ===================== =========================================== ==================================================================== Amino Acid Expands to Comment ===================== =========================================== ==================================================================== B D,N J I,L X A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y The 20 most common amino acids (default) or X A,C,D,E,F,G,H,I,K,L,M,N,O,P,Q,R,S,T,U,V,W,Y All 22 amino acids including the rare Selenocysteine and Pyrrolysine Z E,Q ===================== =========================================== ==================================================================== =================================================== *Degenerate (wild card) deoxyribonucleic acids* =================================================== ===================== ================================ =============================================================================== Deoxyribonucleic Acid Expands to Comment ===================== ================================ =============================================================================== B C,G,T Not A; B follows A alphabetically D A,G,T Not C; D follows C alphabetically H A,C,T Not G; H follows G alphabetically K G,T Keto M A,C aMino N A,C,G,T aNy R A,G puRine S C,G Strong interaction (3 H-bonds) V A,C,G Not T (and not U); V follows U alphabetically W A,T Weak interaction (2 H-bonds) Y C,T pYrimidine ===================== ================================ =============================================================================== =================================================== *Degenerate (wild card) ribonucleic acids* =================================================== ===================== ================================ =============================================================================== Ribonucleic Acid Expands to Comment ===================== ================================ =============================================================================== B C,G,U Not A; B follows A alphabetically D A,G,U Not C; D follows C alphabetically H A,C,U Not G; H follows G alphabetically K G,U Keto M A,C aMino N A,C,G,U aNy R A,G puRine S C,G Strong interaction (3 H-bonds) V A,C,G Not U; V follows U alphabetically W A,U Weak interaction (2 H-bonds) Y C,U pYrimidine ===================== ================================ =============================================================================== ----- **Example** If the degenerate input contains these two peptides:: Seq1 AXY Seq2 SJT The generated FASTA sequences will be this:: >Seq1_1 AAY >Seq1_2 ACY >Seq1_3 ADY >Seq1_4 AEY >Seq1_5 AFY >Seq1_6 AGY >Seq1_7 AHY >Seq1_8 AIY >Seq1_9 AKY >Seq1_10 ALY >Seq1_11 AMY >Seq1_12 ANY >Seq1_13 APY >Seq1_14 AQY >Seq1_15 ARY >Seq1_16 ASY >Seq1_17 ATY >Seq1_18 AVY >Seq1_19 AWY >Seq1_20 AYY >Seq2_1 SIT >Seq2_2 SLT </help> </tool>