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

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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>