galaxy-tool-flash/flash.xml at master · naturalis/galaxy-tool-flash · GitHub

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<tool id="flash merger" name="Merge reads" version="1.1">
<!--
<description>Merge reads</description>
-->
	<requirements>
		<requirement type="package" version="1.2.11">flash</requirement>
		<requirement type="package" version="3.7.0">python</requirement>
		<requirement type="package" version="6.0">unzip</requirement>
		<requirement type="package" version="1.79">biopython</requirement>
	</requirements>
<command>
<![CDATA[
bash '$__tool_directory__/flash.sh'
$input
$output_zip
$output_log
$input2
$allow_outies
$input3
$minoverlap
$mismatch
$maxoverlap]]>

</command>

<inputs>
<param format="zip" name="input" type="data" label="zip file containing fasta or fastq files"/>

				<param name="input2" type="select" multiple="false" label="Input type">
					<option value="gz" selected="true">gzip files</option>
					<option value="FASTQ">fastq files</option>
				</param>
				<param name="minoverlap" type="integer" label="Minimum overlap" value="10" min="1" max="500"/>
				<param name="maxoverlap" type="integer" label="Maximum overlap" value="300" min="1" max="500"/>
				<param name="mismatch" type="float" label="mismatch ratio"  value="0.25" min="0.0" max="1"/>
				<param name="allow_outies" type="boolean" label="Combine read pairs in both orientations" checked="no" truevalue="yes" falsevalue="no"/>
				<param name="input3" type="select" multiple="false" label="Output">
					<option value="discard" selected="true">Output merged reads only</option>
					<option value="add">Add non-merged forward reads to merged reads</option>
					<option value="seperate">Merged reads and non-merged forward reads in seperated files</option>
				</param>
</inputs>


<outputs>
	<data format="zip" type="data" name="output_zip" label="$input.display_name zip" />
	<data format="txt" name="output_log" label="$input.display_name log" />

</outputs>
<tests>
<test>
<param name="test_input" value="test_input.txt"/>
<output name="test_outout" file="test_output.txt"/>
</test>
</tests>
<help>
<![CDATA[
        merge
    ]]>
</help>

	<citations>
	   <citation type="doi">10.1093/bioinformatics/btr507</citation>
	</citations>
</tool>