Mercurial > repos > boris > phylorelatives
changeset 8:e0638858594f draft
Deleted tree structure under test-data
| author | boris |
|---|---|
| date | Wed, 05 Jun 2013 14:04:21 -0400 |
| parents | b73b4f7f5759 |
| children | 663fc7a8549b |
| files | test-data/dependency_configs/tool_dependencies.xml test-data/phylorelatives.xml |
| diffstat | 2 files changed, 0 insertions(+), 127 deletions(-) [+] |
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--- a/test-data/dependency_configs/tool_dependencies.xml Wed Jun 05 13:53:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,14 +0,0 @@ -<tool_dependency> - <package name="R" version="2.15.0"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_r_2_15" owner="boris" changeset_revision="0eb8a25c2c00" /> - </package> - <package name="ape" version="3.0-8"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_ape_3_0" owner="boris" changeset_revision="8dafccd90485" /> - </package> - <package name="rpy2" version="2.2.6"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_rpy2_2_2" owner="boris" changeset_revision="acd114013251" /> - </package> - <package name="dendropy" version="3.12.0"> - <repository toolshed="http://testtoolshed.g2.bx.psu.edu" name="package_dendropy_3_12" owner="boris" changeset_revision="304c2b5f037a" /> - </package> -</tool_dependency>
--- a/test-data/phylorelatives.xml Wed Jun 05 13:53:29 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,113 +0,0 @@ -<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