annotate mzml_to_mgf.xml @ 3:255b5b6ec617 draft default tip

Better defaults for omssa

<tool id="mzml_to_mgf_1" name="MzML to mgf" version="1.0.0">
	<requirements>
		<requirement type="package">protk</requirement>
	</requirements>
	
	<description>Converts an mzML file to mgf suitable for searching by omssa</description>

	<command>file_convert.rb $input_file -o $output $maldi</command>

	<inputs>

		<param name="input_file" type="data" format="mzml"  multiple="false" label="Input File" help="Line Spectra in mzML format"/>
		<param name="maldi" type="boolean" label="Is the data from a MALDI instrument" truevalue="-l" falsevalue=""/>

	</inputs>
	
	<outputs>
		<data format="mgf" name="output" metadata_source="input_file" label="${input_file.display_name}.mgf" from_work_dir="converted.mgf"/>
	</outputs>

	<help>
		Convert line spectra to Mascot Generic Format
	</help>

</tool>