--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/structureharvester.xml	Mon Dec 11 04:37:17 2017 -0500
@@ -0,0 +1,81 @@
+<tool id="structureharvester" name="structureHarvester" version="0.6.94">
+    <description>for parsing STRUCTURE outputs and for performing the Evanno method</description>
+    <requirements>
+        <requirement type="package" version="0.6.94">structureharvester</requirement>
+    </requirements>
+    <version_command><![CDATA[
+        structureHarvester.py --version
+    ]]></version_command>
+    <command detect_errors="exit_code"><![CDATA[
+        mkdir inputs &&
+        #for $input in $inputs
+            ln -s '$input' 'inputs/$input.element_identifier' &&
+        #end for
+        structureHarvester.py --dir inputs/ --out . $evanno $clumpp &&
+        mv summary.txt '$summary'
+        #if $evanno
+            && mv evanno.txt $evanno
+        #end if
+        #if $clumpp
+            && mkdir clumpp_indfile clumpp_popfile
+            && mv *.indfile clumpp_indfile/
+            && mv *.popfile clumpp_popfile/
+        #end if
+    ]]></command>
+    <inputs>
+        <param name="inputs" type="data" format="txt" multiple="true" label="STRUCTURE outputs" />
+        <param argument="--evanno" type="boolean" checked="false" truevalue="--evanno" falsevalue="" label="If possible, performs the Evanno 2005 method." help="You must test at least 3 values of K. K values must be sequential. The number of replicates per K > 1."/>
+        <param argument="--clumpp" type="boolean" checked="false" truevalue="--clumpp" falsevalue="" label="Generates one K*.indfile for each value of K run, for use with CLUMPP." />
+    </inputs>
+    <outputs>
+        <data name="summary" format="txt" label="Structure Harvester summary"/>
+        <data name="evanno" format="txt" label="Evann method output">
+            <filter>evanno</filter>
+        </data>
+        <collection name="clumpp_indfile" type="list" label="Clumpp K*.indfile">
+            <filter>clumpp</filter>
+            <discover_datasets pattern="__name__" format="txt" directory="clumpp_indfile" />
+        </collection>
+        <collection name="clumpp_popfile" type="list" label="Clumpp K*.popfile">
+            <filter>clumpp</filter>
+            <discover_datasets pattern="__name__" format="txt" directory="clumpp_popfile" />
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="inputs" value="example_harvester_archive/Admix_run_001_f,example_harvester_archive/Admix_run_002_f,example_harvester_archive/Admix_run_004_f,example_harvester_archive/Admix_run_005_f,example_harvester_archive/Admix_run_007_f,example_harvester_archive/Admix_run_008_f,example_harvester_archive/K1ReRun_run_1_f,example_harvester_archive/K1ReRun_run_2_f" />
+            <param name="evanno" value="false" />
+            <param name="clumpp" value="true" />
+            <output name="summary">
+                <assert_contents>
+                    <has_line line="1&#009;2&#009;-4329.950000&#009;0.070711" />
+                    <has_line line="4&#009;2&#009;-2773.550000&#009;0.212132" />
+                    <has_line line="K1ReRun_run_2_f&#009;2&#009;1&#009;-4330.0&#009;-4300.2&#009;59.7" />
+                    <has_line line="Admix_run_008_f&#009;008&#009;4&#009;-2773.4&#009;-2678.8&#009;189.2" />
+                    <has_line line="Core version: vA.2 July 2014" />
+                </assert_contents>
+            </output>
+            <output_collection name="clumpp_indfile" type="list">
+                <element name="K1.indfile" value="clumpp_indfile/K1.indfile" />
+                <element name="K4.indfile" value="clumpp_indfile/K4.indfile" />
+            </output_collection>
+            <output_collection name="clumpp_popfile" type="list">
+                <element name="K1.popfile" value="clumpp_popfile/K1.popfile" />
+                <element name="K4.popfile" value="clumpp_popfile/K4.popfile" />
+            </output_collection>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+Structure_Harvester_ is a program for parsing the output of Pritchard's STRUCTURE_ and for performing the Evanno method.
+
+.. _Structure_Harvester: http://taylor0.biology.ucla.edu/structureHarvester/
+.. _STRUCTURE: http://web.stanford.edu/group/pritchardlab/structure.html
+
+    ]]></help>
+    <citations>
+        <citation type="doi">10.1007/s12686-011-9548-7</citation>
+        <citation type="doi">10.1111/j.1365-294X.2005.02553.x</citation>
+        <citation type="doi">10.1093/bioinformatics/btm233</citation>
+    </citations>
+</tool>