--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylogenetic_tree.xml	Mon Apr 09 12:03:06 2012 -0400
@@ -0,0 +1,168 @@
+<tool id="gd_phylogenetic_tree" name="Phylogenetic" version="1.0.0">
+  <description>tree</description>
+
+  <command interpreter="python">
+    phylogenetic_tree.py "$input"
+    #if $individuals.choice == '0'
+      "all_individuals"
+    #else if $individuals.choice == '1'
+      "$p1_input"
+    #end if
+    "$output" "$output.extra_files_path" "$minimum_coverage" "$minimum_quality"
+	#if ((str($input.metadata.scaffold) == str($input.metadata.ref)) and (str($input.metadata.pos) == str($input.metadata.rPos))) or (str($include_reference) == '0')
+        "none"
+    #else
+        "$input.metadata.dbkey"
+    #end if
+    "$data_source"
+    #set $draw_tree_options = ''.join(str(x) for x in [$branch_style, $scale_style, $length_style, $layout_style])
+    #if $draw_tree_options == ''
+        ""
+    #else
+        "-$draw_tree_options"
+    #end if
+    #for $individual_name, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
+        #set $arg = '%s:%s' % ($individual_col, $individual_name)
+        "$arg"
+    #end for
+  </command>
+
+  <inputs>
+    <param name="input" type="data" format="wsf" label="SNP table" />
+
+    <conditional name="individuals">
+      <param name="choice" type="select" label="Individuals">
+        <option value="0" selected="true">All</option>
+        <option value="1">Individuals in a population</option>
+      </param>
+      <when value="0" />
+      <when value="1">
+        <param name="p1_input" type="data" format="ind" label="Population individuals" />
+      </when>
+    </conditional>
+
+    <param name="minimum_coverage" type="integer" min="0" value="0" label="Minimum coverage" help="Note: Minimum coverage and Minimum quality cannot both be 0" />
+
+    <param name="minimum_quality" type="integer" min="0" value="0" label="Minimum quality" help="Note: Minimum coverage and Minimum quality cannot both be 0" />
+
+    <param name="include_reference" type="select" format="integer" label="Include reference sequence">
+      <option value="1" selected="true">Yes</option>
+      <option value="0">No</option>
+    </param>
+
+    <param name="data_source" type="select" format="integer" label="Data source">
+      <option value="0" selected="true">sequence coverage</option>
+      <option value="1">estimated genotype</option>
+    </param>
+
+    <param name="branch_style" type="select" display="radio">
+      <label>Branch type</label>
+      <option value="" selected="true">square</option>
+      <option value="d">diagonal</option>
+    </param>
+     
+    <param name="scale_style" type="select" display="radio">
+      <label>Draw branches to scale</label>
+      <option value="" selected="true">yes</option>
+      <option value="s">no</option>
+    </param>
+     
+    <param name="length_style" type="select" display="radio">
+      <label>Show branch lengths</label>
+      <option value="" selected="true">yes</option>
+      <option value="b">no</option>
+    </param>
+     
+    <param name="layout_style" type="select" display="radio">
+      <label>Tree layout</label>
+      <option value="" selected="true">horizontal</option>
+      <option value="v">vertical</option>
+    </param>
+  </inputs>
+
+  <outputs>
+    <data name="output" format="html" />
+  </outputs>
+
+  <tests>
+    <test>
+      <param name="input" value="test_in/sample.wsf" ftype="wsf" />
+      <param name="choice" value="0" />
+      <param name="minimum_coverage" value="3" />
+      <param name="minimum_quality" value="30" />
+      <param name="data_source" value="0" />
+      <param name="branch_style" value="" />
+      <param name="scale_style" value="" />
+      <param name="length_style" value="" />
+      <param name="layout_style" value="" />
+      <output name="output" file="test_out/phylogenetic_tree/phylogenetic_tree.html" ftype="html" compare="diff" lines_diff="2">
+        <extra_files type="file" name="distance_matrix.phylip" value="test_out/phylogenetic_tree/distance_matrix.phylip" />
+        <extra_files type="file" name="informative_snps.txt" value="test_out/phylogenetic_tree/informative_snps.txt" />
+        <extra_files type="file" name="mega_distance_matrix.txt" value="test_out/phylogenetic_tree/mega_distance_matrix.txt" />
+        <extra_files type="file" name="phylogenetic_tree.newick" value="test_out/phylogenetic_tree/phylogenetic_tree.newick" />
+        <extra_files type="file" name="tree.pdf" value="test_out/phylogenetic_tree/tree.pdf" compare="sim_size" delta = "1000"/>
+      </output>
+    </test>
+  </tests>
+
+  <help>
+**What it does**
+
+This tool uses a SNP table to determine a kind of "genetic distance" between
+each pair of individuals.  Optionally, that information can be used to
+produce a tree-shaped figure that depicts how the individuals are related,
+either as a text file in a common format, called NEWICK, or as a picture.
+The user specifies the following inputs to the tool.
+
+SNP table
+
+Individuals
+  By default, all individuals are included in the analysis; an option
+  is to analyze only a subset of individuals that has been specified
+  using the tool to "Select individuals from a SNP table".
+
+Minimum coverage
+  For each pair of individuals, the tool looks for informative SNPs, i.e.,
+  where the sequence data for both individuals is adequate according to
+  some criterion.  Specifying, say, 7 for this option instructs the tool
+  to consider only SNPs with coverage at least 7 in both individuals
+  when estimating their "genetic distance".
+
+Minimum quality
+  Specifying, say, 37 for this option instructs the tool to consider
+  only SNPs with SAMtools quality value at least 37 in both individuals
+  when estimating their "genetic distance".
+
+Minimum number of informative SNPs
+  This option instructs the tool to terminate execution if at least one
+  pair of individuals does not have a required number of informative SNPs.
+
+Include reference sequence
+  For SNP tables with a reference sequence, the user can ask that the
+  reference be indicated in the tree, to help with rooting it.  If the
+  SNP table has no reference sequence, this option has no effect.
+
+Data source
+  The genetic distance between two individuals at a given SNP can
+  be estimated two ways.  One method is to use the absolute value of
+  difference in the frequency of the first allele (equivalently: the
+  second allele).  For instance, if the first individual has 5 reads of
+  each allele and the second individual has respectively 3 and 6 reads,
+  then the frequencies are 1/2 and 1/3, giving a distance 1/6 at that
+  SNP.  The other approach is to use the SAMtools genotypes to estimate
+  the difference in the number of occurrences of the first allele.
+  For instance, if the two genotypes are 2 and 1, i.e., the individuals
+  are estimated to have respectively 2 and 1 occurrences of the first
+  allele at this location, then the distance is 1 (the absolute value
+  of the difference of the two numbers).
+
+Output format
+  There are three options, as described above.
+
+**Acknowledgments**
+
+To convert the distance matrix to a NEWICK-formatted tree, we use the QuickTree program, downloaded from: http://www.sanger.ac.uk/resources/software/quicktree/
+
+To draw the tree, we use the program draw_tree, downloaded from: http://compgen.bscb.cornell.edu/phast/
+  </help>
+</tool>