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author | boris |
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date | Mon, 03 Feb 2014 13:01:44 -0500 |
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<tool id="phylorelatives" name="Phylorelatives" version="0.0.1"> <description>Relatedness of minor alelle sequences in NJ tree</description> <requirements> <requirement type="package" version="2.15.0">R</requirement> <requirement type="package" version="2.2.6">rpy2</requirement> <requirement type="package" version="3.12.0">dendropy</requirement> <requirement type="package" version="3.0-8">ape</requirement> </requirements> <command interpreter="python">phylorelatives.py #for $sequence in ( $sequences ): -i "${sequence}" #end for -m "${multifasta}" -b "$iterations" $pairwise $major_only #if str($root.root_selector)=="add_root": -r "${root.root_fa}" #end if --relatives-out "$siblings" --newick-out "$newick" --trees-out "$plot" </command> <inputs> <param format="fasta" name="sequences" type="data" label="FASTA file" multiple="TRUE" help="Minor allele sequences must be labeled "_minor" or "_test" e.g. ">sample1_minor""> </param> <conditional name="root"> <param name="root_selector" type="select" label=" Root sequence"> <option value="unrooted" selected="True"></option> <option value="add_root"></option> </param> <when value="unrooted"> </when> <when value="add_root"> <param name="root_fa" format="fasta" type="data" label="Root tree using" help="Must have the same length as input sequences"/> </when> </conditional> <param name="pairwise" type="boolean" truevalue="-p" falsevalue="" checked="False" label="Use pairwise deletion of gaps/missing data" help="Defaults to "Complete deletion""/> <param name="iterations" type="integer" value="1000" label="Change number of bootstrap replicas" help="0 to deactivate"/> <param name="major_only" type="boolean" truevalue="-j" falsevalue="" checked="False" label="Major-alleles-only mode" help="All sequences will be treated as major allele sequences. Useful to generate background tree"/> </inputs> <outputs> <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta used" /> <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives list"/> <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick string"/> <data format="png" name="plot" label="${tool.name} on ${on_string}: tree plot"/> </outputs> <tests> <test> <param name="iterations" value="0"/> <param name="sequences" value="test.fa"/> <output name="siblings" file="test.fa-siblings.tab"/> </test> </tests> <help> The major and minor allele sequences of a sample are expected to cluster together in a phylogenetic tree. Deviation from expectation suggests potential contamination coming from the closest unrelated samples. ----- .. class:: infomark **What it does** Constructs relatedness of a set of sequences based on the pairwise proportion of different sites. One or more test sequences are accepted as long as their name include the strict suffix "_minor" or "_test" (i.e. >seq1_minor). It returns the FASTA multiple alignment used, and reports a table with the closest major allele relatives, the tree plot and newick string of the tree. ----- .. class:: warningmark **Note** This tools DOES NOT align the sequences. Consequently, same length homologous sequences are required as input to fabricate a FASTA multiple alignment by concatenation of individual FASTA files. ----- .. class:: infomark **About formats** *FASTA multiple alignment* See http://www.bioperl.org/wiki/FASTA_multiple_alignment_format *Newick* http://www.megasoftware.net/WebHelp/glossary/rh_newick_format.htm ----- **Example** - For the multiple alignment composed of the following FASTA files:: >sample1_major >sample1_minor >sample2_major >sample3_major >sample4_major - running this tool with *root = RSRS.fasta*, and default parameters will return four datasets:: 1. multiple alignment file used for running the tool 2. relatives of sample1_minor 3. NJ tree newick string (rooted on RSRS) 4. NJ tree png plot (rooted on RSRS) ----- **Citation** If you use this tool, please cite Dickins B, Rebolledo-Jaramillo B, et al. *In preparation.* (boris-at-bx.psu.edu) </help> </tool>