--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bayescan.xml	Fri Mar 17 15:20:38 2017 -0400
@@ -0,0 +1,147 @@
+<tool id="BayeScan" name="BayeScan" version="2.1">
+    <description>Detecting natural selection from population-based genetic data</description>
+    <requirements>
+        <requirement type="package" version="2.0.1">bayescan</requirement>
+    </requirements>
+    <command>
+
+        <![CDATA[
+        mkdir 'output_dir';
+
+        bayescan2 '$input'
+        -od output_dir
+        #if '$loci_file.loci' == "1"
+            -d '$loci_file.input_loci'
+        #end if
+        '$snp_genotypes_matrix'
+        '$fstats'
+        '$pilot_runs'
+        '$allele_frequency'
+        -o bayescan
+        -n '$sample_size'
+        -thin '$thinning_interval'
+        -nbp '$num_pilot_runs'
+        -pilot '$length_pilot_run'
+        -burn '$burn'
+        -pr_odds '$prior_odds'
+        -lb_fis '$lower_prior'
+        -hb_fis '$higher_prior'
+        -aflp_pc '$threshold' > '$output'
+        ]]>
+
+    </command>
+
+    <inputs>
+
+        <param name="input" type="data" format="tabular,txt" label="Input genotype data file" help="must be space/tab delimitted plain text file" />
+        <conditional name="loci_file">
+            <param name="loci" type="select" label="Discard loci?" help="" >
+                <option value="0">No</option>
+                <option value="1">Yes</option>
+            </param>
+            <when value="0"></when>
+            <when value="1">
+                <param name="input_loci" type="data" format="tabular,txt" label="Discard loci file" help="Optional input file containing list of loci to discard" />
+            </when>
+        </conditional>
+        <param name="snp_genotypes_matrix" type="boolean" checked="false" truevalue="-fstat" falsevalue="" label="SNP genotypes matrix data" help="Use SNP genotypes matrix"/>
+
+        <param name="fstats" type="boolean" checked="false" truevalue="-snp" falsevalue="" label="Only estimate F-stats (no selection)"/>
+
+        <param name="sample_size" type="integer" value="5000" label="Number of outputted iterations"/>
+        <param name="thinning_interval" type="integer" value="10" label="Thinning interval size"/>
+        <param name="num_pilot_runs" type="integer" value="20" label="Number of pilot runs" />
+        <param name="length_pilot_run" type="integer" value="5000" label="Length of pilot runs" />
+        <param name="burn" type="integer" value="50000" label="Additional burn-in length" help="Nlength of an interval between two draws in MCMC"/>
+
+        <param name="prior_odds" type="integer" value="10" size="3" label="Prior odds for the neutral model"/>
+        <param name="lower_prior" type="float" value="0.0" label="Lower bound for uniform prior on Fis (dominant data)"/>
+        <param name="higher_prior" type="float" value="1.0" label="Higher bound for uniform prior on Fis (dominant data)"/>
+        <param name="threshold" type="float" value="0.1" label="Threshold for the recessive genotype as a fraction of maximum band intensity"/>
+
+        <param name="pilot_runs" type="boolean" checked="false" truevalue="-out_pilot" falsevalue="" label="Optional output file for pilot runs"/>
+        <param name="allele_frequency" type="boolean" checked="false" truevalue="-out_freq" falsevalue="" label="Optional output file for allele frequencies"/>
+
+
+    </inputs>
+
+    <outputs>
+        <data format="txt"  name="output">
+            <discover_datasets pattern="__designation_and_ext__" directory="output_dir" visible="true" />
+        </data>
+    </outputs>
+
+    <tests>
+        <test>
+            <param name="input" value="test_binary_AFLP.txt" />
+            <param name="loci" value="0" />
+            <param name="snp_genotypes_matrix" value="true" />
+            <param name="fstats" value="true"/>
+
+            <param name="sample_size" value="5000" />
+            <param name="thinning_interval" value="10" />
+            <param name="num_pilot_runs" value="20" />
+            <param name="length_pilot_run" value="5000" />
+            <param name="burn" value="50000" />
+
+            <param name="prior_odds" value="10"/>
+            <param name="lower_prior" value="0.0" />
+            <param name="higher_prior" value="1.0"/>
+            <param name="threshold" value="0.1"/>
+
+            <param name="pilot_runs" value="true"/>
+            <param name="allele_frequency" value="true" />
+
+            <output name="output" file="result.out" ftype="txt">
+                <discovered_dataset designation="bayescan" ftype="sel">
+                    <assert_contents>
+                        <has_text text="logL Fis1 Fis2 Fis3 Fis4 Fis5 Fis6 Fis7 Fis8 Fis9 Fis10 Fst1 Fst2 Fst3 Fst4 Fst5 Fst6 Fst7 Fst8 Fst9 Fst10" />
+                    </assert_contents>
+                </discovered_dataset>
+                <discovered_dataset designation="bayescan_Verif" ftype="txt" value="verif.txt" />
+                <discovered_dataset designation="bayescan_AccRte" ftype="txt">
+                    <assert_contents>
+                        <has_line_matching expression="alpha beta  ances freq   a_p.*" />
+                    </assert_contents>
+                </discovered_dataset>
+                <discovered_dataset designation="bayescan_prop" ftype="txt" value="pilot.txt" />
+                <discovered_dataset designation="bayescan_freq" ftype="txt">
+                    <assert_contents>
+                        <has_text text="locus1 locus2 locus3 locus4 locus5 locus6 locus7 locus8 locus9 locus10" />
+                    </assert_contents>
+                </discovered_dataset>
+            </output>
+        </test>
+    </tests>
+
+    <help><![CDATA[
+
+**What it does**
+
+This program, BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations.
+
+`BayeScan`_ is based on the multinomial-Dirichlet model.
+
+One of the simplest possible scenarios covered consists of an island model in which subpopulation allele frequencies are correlated through a common migrant gene pool from which they differ in varying degrees. The difference in allele frequency between this common gene pool and each subpopulation is measured by a subpopulation specific FST coefficient.
+
+Therefore, this formulation can consider realistic ecological scenarios where the effective size and the immigration rate may differ among subpopulations.
+
+.. _Bayescan: http://cmpg.unibe.ch/software/BayeScan/
+
+.. class:: infomark
+
+**Input file**
+
+BayeScan uses its own input file formats, which depend on the type of data used. All input files are simply in text format.
+
+Read the `manual`_ to create the input file.
+
+.. _manual: http://cmpg.unibe.ch/software/BayeScan/files/BayeScan2.1_manual.pdf
+
+]]>
+
+    </help>
+    <citations>
+        <citation type="doi">10.1534/genetics.108.092221</citation>
+    </citations>
+</tool>