# HG changeset patch
# User boris
# Date 1370455461 14400
# Node ID e0638858594fbdb099fbe697cf77224d55a2246e
# Parent  b73b4f7f5759b7ddc3f26bd193990969bf7b71a6
Deleted tree structure under test-data

diff -r b73b4f7f5759 -r e0638858594f test-data/dependency_configs/tool_dependencies.xml
--- 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>
diff -r b73b4f7f5759 -r e0638858594f test-data/phylorelatives.xml
--- 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 &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>
\ No newline at end of file