comparison alfa/ALFA.xml @ 46:5d745637f045 draft default tip

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45:f4b26211e3d8

				<when value="personal_gtf">
					<param name="annotationFile" type="data" format="Gff, Gtf" label="Select your personal annotation file (GTF format)">
					</param>
				</when>
				<when value="index">
					<param name="strandedIndex" type="data" format="index" label="Select your ALFA Stranded index file (index format)"/>
					<param name="unstrandedIndex" type="data" format="index" label="Select your ALFA Unstranded index file (index format)"/>
				</when>
				<when value="built_in_index">
					<param name="built_in_index_prefix" type="select" label="Select Genome">
						<options from_data_table="alfa_indexes">
							<validator type="no_options" message="No indexes are available for the selected input dataset. Ask your Galaxy Admin for to use ALFA_data_manager tool to build such indexes!" />

				<option value="2">exon | intron | undescribed genes | intergenic | antisense</option>
				<option value="3" selected="true">5’-UTR | CDS | 3’-UTR | underscribes exons | intron | undescribed genes | intergenic | antisense</option>
				<option value="4">5’-UTR | start_codon | CDS | undescribed CDS | stop_codon | 3’-UTR | undescribed exons | intron | undescribed genes | intergenic | antisense</option>
			</param>
			<param name="plotFormat" type="select" label="Plot Options: Select graph format" help="Ignore if you did not choose the histograms output file">
				<option value="pdf" selected="true">pdf</option>
				<option value="svg">svg</option>
				<option value="png">png</option>
			</param>
			<conditional name="plotThreshold">
				<param name="plotThresholdChoice" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Plot Options: Modify y axis range of the normalized counts of bio-features" help="Ignore if you did not choose the histograms output file"/>
					<when value="True">
						<param name="yMin" type="float" value="-2.0" label="y min"/>

		</section>
	</inputs>
	
	<outputs>
		<data name="logReport" format="txt" label="${projectName}-Log Report"/>
		<data name="outputPdf" format="pdf" label="${projectName}-BioFeatures Distribution">
			<filter>outputFiles['plot'] is True and outputOptions['plotFormat'] == 'pdf'</filter>
		</data>
		<data name="outputCategoriesPng" format="png" label="${projectName}-Categories Distribution">
			<filter>outputFiles['plot'] is True and outputOptions['plotFormat'] == 'png'</filter>
		</data>
		<data name="outputBiotypesPng" format="png" label="${projectName}-Biotypes Distribution">
			<filter>outputFiles['plot'] is True and outputOptions['plotFormat'] == 'png'</filter>

46:5d745637f045

				<when value="personal_gtf">
					<param name="annotationFile" type="data" format="Gff, Gtf" label="Select your personal annotation file (GTF format)">
					</param>
				</when>
				<when value="index">
					<param name="strandedIndex" type="data" label="Select your ALFA Stranded index file (index format)"/>
					<param name="unstrandedIndex" type="data" label="Select your ALFA Unstranded index file (index format)"/>
				</when>
				<when value="built_in_index">
					<param name="built_in_index_prefix" type="select" label="Select Genome">
						<options from_data_table="alfa_indexes">
							<validator type="no_options" message="No indexes are available for the selected input dataset. Ask your Galaxy Admin for to use ALFA_data_manager tool to build such indexes!" />

				<option value="2">exon | intron | undescribed genes | intergenic | antisense</option>
				<option value="3" selected="true">5’-UTR | CDS | 3’-UTR | underscribes exons | intron | undescribed genes | intergenic | antisense</option>
				<option value="4">5’-UTR | start_codon | CDS | undescribed CDS | stop_codon | 3’-UTR | undescribed exons | intron | undescribed genes | intergenic | antisense</option>
			</param>
			<param name="plotFormat" type="select" label="Plot Options: Select graph format" help="Ignore if you did not choose the histograms output file">
				<option value="png"  selected="true">png</option>
				<!--<option value="pdf" selected="true">pdf</option>-->
				<option value="svg">svg</option>
			</param>
			<conditional name="plotThreshold">
				<param name="plotThresholdChoice" type="boolean" truevalue="True" falsevalue="False" checked="false" label="Plot Options: Modify y axis range of the normalized counts of bio-features" help="Ignore if you did not choose the histograms output file"/>
					<when value="True">
						<param name="yMin" type="float" value="-2.0" label="y min"/>

		</section>
	</inputs>
	
	<outputs>
		<data name="logReport" format="txt" label="${projectName}-Log Report"/>
		<!--
		<data name="outputPdf" format="pdf" label="${projectName}-BioFeatures Distribution">
			<filter>outputFiles['plot'] is True and outputOptions['plotFormat'] == 'pdf'</filter>
		</data>
		-->
		<data name="outputCategoriesPng" format="png" label="${projectName}-Categories Distribution">
			<filter>outputFiles['plot'] is True and outputOptions['plotFormat'] == 'png'</filter>
		</data>
		<data name="outputBiotypesPng" format="png" label="${projectName}-Biotypes Distribution">
			<filter>outputFiles['plot'] is True and outputOptions['plotFormat'] == 'png'</filter>