comparison tassel.xml @ 6:28c0efb3a226 draft

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5:e94b8b64929c

<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":
  -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait

 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
#else if $analysis_opts.fonction_selector == "ck":
 -fork1 -h $hapmap
 -ck -export tmpdir$$/kinship -runfork1
#end if
	</command>
	<inputs>
		<param format="txt" name="hapmap" type="data" label="HapMap file"/>
		<conditional name="analysis_opts">
			<param name="fonction_selector" type="select" label="Type of analysis">
				<option value="mlm" selected="True">MLM</option>

			<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="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>

6:28c0efb3a226

<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>
				<requirement type="package" version="1.8">openjdk</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 detect_errors="exit_code"><![CDATA[./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":
  -fork3 -q $analysis_opts.add_structure_file.structure -excludeLastTrait

 -ld -ldType All -ldd png -ldplotsize 3000 -o $output1 -runfork1
#else if $analysis_opts.fonction_selector == "ck":
 -fork1 -h $hapmap
 -ck -export tmpdir$$/kinship -runfork1
#end if
	]]></command>
	<inputs>
		<param format="txt" name="hapmap" type="data" label="HapMap file"/>
		<conditional name="analysis_opts">
			<param name="fonction_selector" type="select" label="Type of analysis">
				<option value="mlm" selected="True">MLM</option>

			<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="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>