--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ks_distribution.xml	Mon May 01 13:47:20 2017 -0400
@@ -0,0 +1,110 @@
+<tool id="ks_distribution" name="KsDistribution" version="1.0.0">
+    <description>plots the distribution of synonymous substitution (Ks) rates and fits significant componets(s)</description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements_ks_distribution" />
+    <expand macro="stdio" />
+    <command>
+        <![CDATA[
+            Rscript $__tool_directory__/ks_distribution.R
+            -k '${kaks}'
+            -c '${components}'
+            -o '$output'
+        ]]>
+    </command>
+    <inputs>
+        <param name="rates" format="tabular" type="data" label="Synonymous substitution rates" />
+        <param name="components" format="tabular" type="data" label="Significant components" />
+    </inputs>
+    <outputs>
+        <data name="output" format="pdf"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="rates" value="rates.tabular" ftype="tabular" />
+            <param name="components" value="components.tabular" ftype="tabular" />
+            <output name="output" file="output.pdf" ftype="pdf" compare="contains" />
+        </test>
+    </tests>
+    <help>
+**What it does**
+ 
+This tool is one of the PlantTribes collection of automated modular analysis pipelines for comparative and evolutionary analyses of
+genome-scale gene families and transcriptomes.  This tool uses the analysis results produced by the KaKsAnalysis tool to plot the
+distribution of synonymous substitution (Ks) rates and fit the estimated significant normal mixtures component(s) onto the distribution.
+
+-----
+
+**Options**
+
+ * **Required**
+
+  - **Synonymous substitution rates** - estimated synonymous substitution (Ks) rates output file produced by the KaKsAnalysis tool selected from your history.
+  - **Synonymous components** - estimated significant component(s) output file produced by the KaKsAnalysis tool selected from your history.
+    </help>
+    <citations>
+        <expand macro="citation1" />
+        <citation type="bibtex">
+            @article{Wall2008,
+            journal = {Nucleic Acids Research},
+            author = {2. Wall PK, Leebens-Mack J, Muller KF, Field D, Altman NS},
+            title = {PlantTribes: a gene and gene family resource for comparative genomics in plants},
+            year = {2008},
+            volume = {36},
+            number = {suppl 1},
+            pages = {D970-D976},}
+        </citation>
+        <citation type="bibtex">
+            @article{Altschul1990,
+            journal = {Journal of molecular biology}
+            author = {3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ},
+            title = {Basic local alignment search tool},
+            year = {1990},
+            volume = {215},
+            number = {3},
+            pages = {403-410},}
+        </citation>
+        <citation type="bibtex">
+            @article{Katoh2013,
+            journal = {Molecular biology and evolution},
+            author = {4. Katoh K, Standley DM},
+            title = {MAFFT multiple sequence alignment software version 7: improvements in performance and usability},
+            year = {2013},
+            volume = {30},
+            number = {4},
+            pages = {772-780},}
+        </citation>
+        <citation type="bibtex">
+            @article{Yang2007,
+            journal = {Molecular biology and evolution},
+            author = {5. Yang Z},
+            title = {PAML 4: phylogenetic analysis by maximum likelihood},
+            year = {2007},
+            volume = {24},
+            number = {8},
+            pages = {1586-1591},}
+        </citation>
+        <citation type="bibtex">
+            @article{Cui2006,
+            journal = {Genome Research},
+            author = {6. Cui L, Wall PK, Leebens-Mack JH, Lindsay BG, Soltis DE, Doyle JJ, Soltis PS, Carlson JE, Arumuganathan K, Barakat A, Albert VA},
+            title = {Widespread genome duplications throughout the history of flowering plants},
+            year = {2006},
+            volume = {16},
+            number = {6},
+            pages = {738-749},}
+        </citation>
+        <citation type="bibtex">
+            @article{McLachlan1999,
+            journal = {Journal of Statistical Software},
+            author = {7. McLachlan GJ, Peel D, Basford KE, Adams P},
+            title = {The EMMIX software for the fitting of mixtures of normal and t-components},
+            year = {1999},
+            volume = {4},
+            number = {2},
+            pages = {1-14},}
+        </citation>
+    </citations>
+</tool>
+