comparison tassel.xml @ 4:652aafd88060 draft

planemo upload commit 475f4d7d8442a0d75e103af326ae5881c4d2a4ac

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<tool id="Tassel" name="Tassel" version="5.0">
	<description> Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium. </description>
	<requirements>
                <requirement type="package" version="5.0">tassel</requirement>
        </requirements>
	<command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
#if $analysis_opts.fonction_selector == "mlm":
 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
 -fork2 -r $analysis_opts.trait
 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":

                	                	<option value="yes">yes</option>
	                	        </param>
					<when value="yes">
						<param format="txt" name="structure" type="data" label="Structure file"/>
					</when>
				</conditional>
			</when>
			<when value="mlm">
                		<param format="txt" name="trait" type="data" label="Trait file"/>
		                <param format="txt" name="kinship" type="data" label="Kinship file"/>

                	                	<option value="yes">yes</option>
	                	        </param>
					<when value="yes">
						<param format="txt" name="structure" type="data" label="Structure file"/>
					</when>
				</conditional>
				<param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
					<option value="P3D" selected="True">P3D</option>
					<option value="EachMarker">EachMarker</option>
				</param>

			<filter>analysis_opts['fonction_selector'] == "mlm"</filter>
		</data>
		
		<data format="txt" name="log" label="Log file"/>
	</outputs>
	<help>

.. class:: infomark

**Program encapsulated in Galaxy by Southgreen**

.. class:: infomark

**Tassel**

-----

==========
 Authors:
==========

**Terry Casstevens**

-----

==========
 Overview
==========

Software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.

-----

For further informations, please visite the website of TASSEL_.


.. _TASSEL: http://www.maizegenetics.net/tassel/

	</help>
<!--
<tests>
  <test>
      <param name="input" value="genotyping_file.inp" />
      <output name="output" file="phase_output" />
   </test>
</tests>
-->
</tool>

4:652aafd88060

<tool id="Tassel" name="Tassel" version="2.0.0">
	<description>Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium</description>
	<requirements>
                <requirement type="package" version="5.2.40">tassel</requirement>
        </requirements>

    <stdio>
        <!-- [HELP] If no exit code rule is defined, the tool will stop if anything is written to STDERR -->
        <exit_code range="1:" level="fatal" />
    </stdio>

	<command interpreter="bash">./tassel.sh $analysis_opts.fonction_selector $output1 $output2 $output3 $log tmpdir$$/
#if $analysis_opts.fonction_selector == "mlm":
 -fork1 -h $hapmap -filterAlign -filterAlignMinFreq $filterAlignMinFreq
 -fork2 -r $analysis_opts.trait
 #if $analysis_opts.add_structure_file.additional_file_selector == "yes":

                	                	<option value="yes">yes</option>
	                	        </param>
					<when value="yes">
						<param format="txt" name="structure" type="data" label="Structure file"/>
					</when>
                                        <when value="no">
                                        </when>
				</conditional>
			</when>
			<when value="mlm">
                		<param format="txt" name="trait" type="data" label="Trait file"/>
		                <param format="txt" name="kinship" type="data" label="Kinship file"/>

                	                	<option value="yes">yes</option>
	                	        </param>
					<when value="yes">
						<param format="txt" name="structure" type="data" label="Structure file"/>
					</when>
                                        <when value="no">
                                        </when>
				</conditional>
				<param name="mlmVarCompEst" type="select" label="Variance Component Estimation">
					<option value="P3D" selected="True">P3D</option>
					<option value="EachMarker">EachMarker</option>
				</param>

			<filter>analysis_opts['fonction_selector'] == "mlm"</filter>
		</data>
		
		<data format="txt" name="log" label="Log file"/>
	</outputs>

    <tests>
        <test>
            <param name="hapmap" value="input_hapmap.txt"/>
            <conditional name="analysis_opts">
                <param name="fonction_selector" value="glm"/>
                <param name="trait" value="phenotyping_DRB.csv"/>
                <conditional name="add_structure_file">
                    <param name="additional_file_selector" value="yes"/>
                    <param name="structure" value="Best_K_Output"/>
                </conditional>
            </conditional>
            <param name="filterAlignMinFreq" value="0.05"/>
            <output name="output1" value="Tassel_output.txt"/>
            <output name="output2" value="Allele_effects.txt"/>
        </test>
    </tests>

    <help><![CDATA[


.. class:: infomark

**Tassel5** version 5.2.40

.. class:: infomark

**Galaxy integration** Provided by Southgreen & Dereeper Alexis (IRD) & Marcon Valentin (IFB & INRA)

.. class:: infomark

**Support** For any questions about Galaxy integration, please send an e-mail to [e-mail]

---------------------------------------------------

=======
Tassel5
=======

-----------
Description
-----------

  | Software to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
  | For further informations on tassel, please visit the website_.

.. _website: http://www.maizegenetics.net/tassel/

------------
Dependencies
------------
Tassel5
        tassel_ 5.2.40, Conda version

.. _tassel: https://anaconda.org/bioconda/tassel

    ]]></help>
    <citations>
       <citation type="doi">10.1093/bioinformatics/btm308</citation>
    </citations>
</tool>