Mercurial > repos > boris > phylorelatives
changeset 6:053eddf670bb draft
fixed dendropy version dependency in tool xml
author | boris |
---|---|
date | Wed, 05 Jun 2013 13:51:19 -0400 |
parents | 29fa7e1072cb |
children | b73b4f7f5759 |
files | test-data/phylorelatives.xml |
diffstat | 1 files changed, 113 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/phylorelatives.xml Wed Jun 05 13:51:19 2013 -0400 @@ -0,0 +1,113 @@ +<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.sequence}" + #end for + -m "${multifasta}" + -b "$iterations" + $pairwise + #if str($root.root_selector)=="upload_root": + -r "${root.root_fa}" + #end if + --relatives-out "$siblings" + --newick-out "$newick" + --trees-out "$plot" + + </command> + <inputs> + <repeat name="sequences" title="Input FASTA file" min="1" help="Files will be concatenated into a single FASTA multiple alignment file, thus equal length homologous sequences are required"> + <param format="fasta" name="sequence" type="data" label="FASTA file" help="Requires at least one minor allele sequence properly labeled "_minor" or "_test" e.g. ">sample1_minor""> + </param> + </repeat> + <conditional name="root"> + <param name="root_selector" type="select" label=" Root sequence"> + <option value="unrooted" selected="True"></option> + <option value="upload_root"></option> + </param> + <when value="unrooted"> + </when> + <when value="upload_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"/> + </inputs> + <outputs> + <data format="fasta" name="multifasta" label="${tool.name} on ${on_string}: multifasta" /> + <data format="tabular" name="siblings" label="${tool.name} on ${on_string}: relatives"/> + <data format="txt" name="newick" label="${tool.name} on ${on_string}: newick"/> + <data format="png" name="plot" label="${tool.name} on ${on_string}: plot"/> + </outputs> + <tests> + <test> + <param name="iterations" value="0"/> + <param name="sequence" value="test.fa"/> + <output name="siblings" file="test.fa-siblings.tab"/> + </test> + </tests> + + <help> + + + + +(boris-at-bx.psu.edu) + + +----- + +.. 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 relatives of the minor allele sequence in a NJ tree, the tree plot and newick string. + +----- + +.. class:: warningmark + +**Note** + +This tools DOES NOT align the sequences. +The FASTA multiple alignment file is fabricated by concatenating same length homologous sequences. +An independently aligned FASTA multiple alignment file can be used as well. + +----- + +.. class:: infomark + +**About formats** + +**FASTA multiple alignment** -- + +describe format shortly + +----- + +**Example** + +- For the following dataset:: + >sample1_major + >sample1_minor + >sample2_major + >sample3_major + >sample4_major + + +- running this tool with **b = 1000** **m = yes** **root = RSRS**, will return:: + newick + relatives + plot + </help> + +</tool> \ No newline at end of file