view imgt_concatenate.xml @ 6:dc86c36161d0 draft default tip

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<tool id="imgt_concatenate" name="IMGT Concatenate" version="1.0">
	<description> </description>
	<command interpreter="bash">
		imgt_concatenate.sh $out_file 
#if str( $with_id.with_id_selector ) == "true":
	#for $i, $f in enumerate($with_id.files)
	 "$f.file"
	 "$f.id"
	#end for
#else
	#for $i, $f in enumerate($with_id.files)
	 "$f.file"
	 ""
	#end for
#end if
	</command>
	<inputs>
		<conditional name="with_id">
			<param name="with_id_selector" type="select" label="Add a file ID to the sequence ID">
				<option value="true">Add file ID to SequenceID to identify the origin file</option>
				<option value="false" selected="True">Keep SequenceID as is</option>
			</param>
			<when value='true'>
				<repeat name="files" title="Sample" min="2" default="2">
					<param name="file" type="data" format="data" label="IMGT zip file" />
					<param name="id" type="text" label="File ID" size="25">
						<validator type="regex" message="Fill in an ID">.+</validator>
					</param>
				</repeat>
			</when>
			<when value='false'>
				<repeat name="files" title="Sample" min="2" default="2">
					<param name="file" type="data" format="data" label="IMGT zip file" />
				</repeat>
			</when>
		</conditional>
		<param name="label" type="text" label="A name for the new dataset" size="25">
			<validator type="regex" message="Fill in a name for the new dataset">.+</validator>
		</param>
	</inputs>
	<outputs>
		<data format="data" name="out_file" label="${label}"/>
	</outputs>
	<help>
Concatenate two or more IMGT files to create one new IMGT zip with all the sequences of the inputs.

	</help>

</tool>