view phylorelatives.xml @ 9:663fc7a8549b draft

uploaded tool xml

<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 &quot;_minor&quot; or &quot;_test&quot; e.g. &quot;>sample1_minor&quot;">
      </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 &quot;Complete deletion&quot;"/>
    <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>