comparison vst_transformation.xml @ 0:a48dde9abecf draft

Uploaded initial version

0:a48dde9abecf

<tool id="vsttransform" name="Variance stabilizing transformation" version="1.0.0">
    <description>
		using DESeq
    </description>
    
    <requirements>
		<requirement type="package" version="3.0.1">package_r3</requirement>
		<requirement type="package" version="1.0.0">r_additions</requirement>
		<requirement type="package" version="2.12">biocbasics</requirement>
	</requirements>
    
    <command interpreter="perl">
		vst_transformation.pl ${parameters}
    </command> 
   
    <inputs>
	<param format="tabular" name="counttable" type="data" label="Count table" help="Count table generated by HTSeq-count on mapped RNA-seq data" /> 
	<param name="header_row" type="boolean" checked="TRUE" truevalue="TRUE" falsevalue="FALSE" label="Does the table has a header row" /> 
	<param name="header_columns" type="boolean" checked="TRUE" truevalue="TRUE" falsevalue="FALSE"  label="Does the first column contains identifiers" /> 
	
	<repeat name="replicates" title="Replicate group">
		<param name="repl_group_name" type="text" value="" size="50" label="Replicate group name">
			<sanitizer invalid_char="">
				<valid initial="string.letters,string.digits"><add value="_" /> </valid>
			</sanitizer>
		</param>
		<param name="rep_columns" label="Select replicates" type="data_column" data_ref="counttable" numerical="True" 
	         		multiple="true" use_header_names="true" size="120" display="checkboxes">
        		<validator type="no_options" message="Please select at least one column."/>
		</param>  <!-- $replicates contains a comma-separated list of number -->
	</repeat>
    </inputs>

    <outputs>
		<data format="tabular" name="outtab" label="${tool.name} of ${on_string}"/>
		<data format="html" name="html_file" label="Histogram of ${tool.name} of ${on_string}"/>		
    </outputs>

	<configfiles>
		<configfile name="parameters">
			## first we pass some galaxy environment variables
			counttable==$counttable
			header_row==$header_row
			header_columns==$header_columns
			outtab==$outtab
			html_file==$html_file
			
			##REPEAT BLOCK
			#for $i, $s in enumerate( $replicates )
			replicates_$s.repl_group_name==$s.rep_columns
			#end for
		</configfile>

	</configfiles> 

	<tests>
		<test>
			<param name="counttable" value="counttable1.tsv" ftype="tabular" />
			<param name="header_row" value="TRUE" />
			<param name="header_columns" value="TRUE" />
			<param name="repl_group_name" value="can" />
			<param name="rep_columns" value="2,3" />
			<output name="outtab" file="vst_transf_tabout.txt" ftype="tabular" />
			<output name="html_file" file="vst_transf_htmlout.html" ftype="html" lines_diff="6"/>
		</test>
	</tests>

    <help>
**Variance stabilizing transformation**

This tool takes in raw count data per feature and applies a variance stabilizing transformation using DESeq.
    </help>
</tool>