view split_15/split7_15nodes.xml @ 0:1cbba720061a draft

Uploaded

<tool id="split7_15nodes" name="Split e-traits" version="7.0.0">
	<description> into 15 sub-files</description>
	<command interpreter="python">
            split7_15nodes.py --input1 $input1 --input2 $input2 --input3 $input3 --SRmodel $SRmodel --Zmodel $Zmodel --threshold $threshold --walking_speed $walking_speed --window_size $window_size --minimum_cM_between_QTL $minimum_cM_between_QTL --output1 $output1 --output2 $output2 --output3 $output3 --output4 $output4 --output5 $output5 --output6 $output6 --output7 $output7 --output8 $output8 --output9 $output9 --output10 $output10 --output11 $output11 --output12 $output12 --output13 $output13 --output14 $output14 --output15 $output15 --output16 $output16
	</command>
        <inputs>
            <param label="Expression traits (etraits) file" name="input1" type="data" format="tabular" help="A tabular file with the phenotype information"></param>
	    <param label="Other traits (otraits) file" name="input2" type="data" format="tabular" help="A tabular file with the other trait information"></param>
	    <param label="Phenotype-genotype (.inp) file" name="input3" type="data" format="txt" help="A .inp file with all genotype and phenotype information"></param>
	    <param name="SRmodel" label="Stepwise regression model: 0=SF, 1=EB, 2=FB (default)" value="2" type="integer" help="Select the stepwise regression model to search for QTLs: 0=SF, 1=EB, 2=FB (default)">
		<validator type="in_range" message="Number can be 0, 1 or 2" min="0" max="2"/>
		<validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
	    </param>
	    <param name="Zmodel" label="Model for interval mapping: 3=IM or 6=CIM (default)" value="6" type="integer" help="Select interval mapping (3) or composite interval mapping (6, default)">
		<validator type="in_range" message="Number can be 3 or 6" min="3" max="6"/>
		<validator type="expression" message="An integer is required.">int( float( value ) ) == float( value )</validator>
	    </param>
	    <param name="threshold" label="LR threshold" value="11.5" type="float" help="Select a LR threshold (default=11.5)">
		<validator type="in_range" message="Float can be between 0 and 100" min="0" max="100"/>
		<validator type="expression" message="A float is required.">float( float( value ) ) == float( value )</validator>
	    </param>
	    <param name="walking_speed" label="Walking speed in cM" value="2.0" type="float" help="Select a walking speed in cM (default=2.0)">
		<validator type="in_range" message="Float can be between 0 and 10" min="0" max="10"/>
		<validator type="expression" message="A float is required.">float( float( value ) ) == float( value )</validator>
	    </param>
	    <param name="window_size" label="Window size in cM" value="10.0" type="float" help="Select a window size in cM (default=10.0)">
		<validator type="in_range" message="Float can be between 0 and 50" min="0" max="50"/>
		<validator type="expression" message="A float is required.">float( float( value ) ) == float( value )</validator>
	    </param>
	    <param name="minimum_cM_between_QTL" label="Minimum cM between QTL" value="20.0" type="float" help="Select a minimum cM between QTL (default=20.0)">
		<validator type="in_range" message="Float can be between 0 and 50" min="0" max="50"/>
		<validator type="expression" message="A float is required.">float( float( value ) ) == float( value )</validator>
	    </param>
        </inputs>
	<outputs>
                <data format="txt" name="output1" />
		<data format="txt" name="output2" />
		<data format="txt" name="output3" />
		<data format="txt" name="output4" />
		<data format="txt" name="output5" />
                <data format="txt" name="output6" />
                <data format="txt" name="output7" />
		<data format="txt" name="output8" />
		<data format="txt" name="output9" />
		<data format="txt" name="output10" />
                <data format="txt" name="output11" />
		<data format="txt" name="output12" />
		<data format="txt" name="output13" />
		<data format="txt" name="output14" />
		<data format="txt" name="output15" />
                <data format="txt" name="output16" />
	</outputs>
	<requirements>
	</requirements>
	<tests>
          <test>
          </test>
	</tests>
	<help>
		
**What it does**

Splits the input phenotype data into smaller .inp files.

This makes 15 parallel runs on the cluster possible, to reduce the running time of large phenotype datasets (e.g. eQTL data sets). 

        </help>
</tool>