diff structure-923cc9e6aa30/Structureharvester.xml @ 0:2c0b270dae70 draft default tip

Uploaded

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+++ b/structure-923cc9e6aa30/Structureharvester.xml	Thu Sep 14 08:33:05 2017 -0400
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+<tool id="Structureharvester" name="Structure harvester"  force_history_refresh="True">
+  <description>Run the structureharvester.py script</description>
+
+
+<configfiles>
+<configfile name="Structure_archive">
+#for $input in $Structure_archive:
+${input.display_name}::${input}
+#end for
+</configfile>
+</configfiles>
+
+<command interpreter="python">
+
+Structureharvester.py
+-P $Structure_archive
+#if str( $options_output.options_output_selector ) == "1":
+--evanno $options_output.evanno
+--clumpp $options_output.clumpp
+#end if
+--logfile $output
+--id $output.id
+--workdir $__new_file_path__
+--compress_output $output_compress
+--total_output $total_output
+
+
+
+</command>
+
+<inputs>
+	<param name="Structure_archive" format="zip,tar.gz" type="data"  multiple="true" label="Archive from Structure analysis regrouping all outputs" />
+	<conditional name="options_output">
+	    <param name="options_output_selector" type="select" label="Did you want to use file output options?">
+			<option value="1">Yes</option>
+			<option value="2" selected="true">No</option>
+	    </param>
+	    <when value="1">
+			<param name="evanno" type="boolean" checked="false" default="false" label="If possible, performs the Evanno 2005 method" />
+			<param name="clumpp" type="boolean" checked="false" default="false" label="Generates one K*.indfile for each value of K run, for use with CLUMPP" />
+	    </when>
+	    <when value="2">
+	    </when>
+	</conditional>
+
+
+	<!-- Output options -->
+	<param name="output_compress" type="select" label="Output type" help="please see below for details">
+		<option value="default" selected="true">No compression</option>		
+		<option value="total">Compressed all outputs</option>
+	</param>
+</inputs>
+<outputs>
+
+    <data format="txt" name="output" label="result with ${tool.name} on ${on_string}" />
+
+    <!-- additionnal output archives -->
+    <data format="zip" name="total_output" label="total_output.zip with ${tool.name} on ${on_string}" >
+        <filter>output_compress == "total"</filter>
+    </data>
+
+
+</outputs>
+<help>
+
+.. class:: infomark
+
+**What it does**
+
+This program (structureHarvester.py) is a Python script capable of extracting all the relevant data from STRUCTURE results files.
+
+--------
+
+**Created by:**
+
+structureHarvester.py was developed by Dent Earl,  soe ucsc edu
+
+--------
+
+
+Instructions to add the functionality of archives management in Galaxy on the `eBiogenouest HUB wiki &lt;https://www.e-biogenouest.org/wiki/ManArchiveGalaxy&gt;`_ .
+
+--------
+
+**Project links:**
+
+`Structure Harvester website &lt;http://users.soe.ucsc.edu/~dearl/software/structureHarvester/&gt;`_ .
+
+--------
+
+**References:**
+
+-Earl, Dent A. and vonHoldt, Bridgett M. (2012) STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources vol. 4 (2) pp. 359-361 doi: 10.1007/s12686-011-9548-7
+
+-Evanno et al., 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14 , 2611 - 2620.
+
+-M. Jakobsson, N. Rosenberg 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14): 1801-1806.
+
+-J. Pritchard, M. Stephens, P. Donnelly. 2000. Genetics 155:945-959.
+
+--------
+
+**Integrated by:**
+
+Yvan Le Bras
+
+GenOuest Bio-informatics Core Facility
+
+UMR 6074 IRISA INRIA-CNRS-UR1 Rennes (France)
+
[e-mail]
+
+If you use this tool in Galaxy, please cite :
+
+`Y. Le Bras, A. Roult, C. Monjeaud, M. Bahin, O. Quenez, C. Heriveau, A. Bretaudeau, O. Sallou, O. Collin, Towards a Life Sciences Virtual Research Environment : an e-Science initiative in Western France. JOBIM 2013. &lt;https://www.e-biogenouest.org/resources/128&gt;`_
+
+
+
+</help>
+</tool>
+