comparison VCFToolsSlidingWindow/vcfToolsSlidingWindow.xml @ 4:b762ecbe2314 draft

planemo upload

3:612066e3f57d

    </stdio>
    
    
    <!-- [REQUIRED] The command to execute -->
    <command interpreter="bash">
    	vcfToolsSlidingWindow.sh ${filein} $step $window $filelog ${fileout_taj} ${fileout_tstv} ${fileout_windowed} ${fileout_snp} 
	#if  $group :
	$group ${fileout_fst} ${fileout_fst_marker}  ${fileout_taj_combined} ${fileout_windowed_combined}
	#else : 
	"none"
	#end if

    <!-- [REQUIRED] Input files and tool parameters -->
    <inputs>
	<param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
	<param name="fileout_label" type="text" value="snp_density" optional="false" label="Output file basename"/>
	<param name="window" type="integer" value="200000" optional="false" label="Window size (in bp)"/>
	<param name="step" type="integer" value="50000" optional="false" label="Step size (in bp)"/>
	<param name="group" type="data" format="tab" optional="True" label="(optionnal) Groups" help="Each line of the file should be : Indiv;Pop" />
    </inputs>
    
    <!-- [REQUIRED] Output files -->
    <outputs>

    
    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
    <tests>
        <!-- [HELP] Test files have to be in the ~/test-data directory -->
	<test>
         <param name="filein" value="sample_group.vcf" />
	 <param name="group" value="groups.txt" />
         <output name="fileout_snp" file="result2.snpden" />
         <output name="fileout_taj" file="result2.Tajima.D" />
         <output name="fileout_tstv" file="result2.TsTv" />
         <output name="fileout_windowed" file="result2.windowed.pi" />
	 <output name="fileout_fst" file="result2.fst.txt" />
         <output name="fileout_fst_marker" file="result2.fst.by_marker.genes.txt" />
         <output name="fileout_taj_combined" file="result2.combined.dtajima.txt" />
         <output name="fileout_windowed_combined" file="result2.combined.pi.txt" />
        </test>
	<test>
         <param name="filein" value="sample.vcf" />
         <output name="fileout_snp" file="result.snpden" />
         <output name="fileout_taj" file="result.Tajima.D" />
         <output name="fileout_tstv" file="result.TsTv" />
         <output name="fileout_windowed" file="result.windowed.pi" />
        </test>
    </tests>
    
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <help>

4:b762ecbe2314

    </stdio>
    
    
    <!-- [REQUIRED] The command to execute -->
    <command interpreter="bash">
    	vcfToolsSlidingWindow.sh ${filein} $window $filelog ${fileout_taj} ${fileout_tstv} ${fileout_windowed} ${fileout_snp} 
	#if  $group :
	$group ${fileout_fst} ${fileout_fst_marker}  ${fileout_taj_combined} ${fileout_windowed_combined}
	#else : 
	"none"
	#end if

    <!-- [REQUIRED] Input files and tool parameters -->
    <inputs>
	<param name="filein" type="data" format="vcf" optional="false" label="VCF input" />
	<param name="fileout_label" type="text" value="snp_density" optional="false" label="Output file basename"/>
	<param name="window" type="integer" value="200000" optional="false" label="Window size (in bp)"/>
	<param name="group" type="data" format="tab" optional="True" label="(optionnal) Groups" help="Each line of the file should be : Indiv;Pop" />
    </inputs>
    
    <!-- [REQUIRED] Output files -->
    <outputs>

    
    <!-- [OPTIONAL] Tests to be run manually by the Galaxy admin -->
    <tests>
        <!-- [HELP] Test files have to be in the ~/test-data directory -->
	<test>
         <param name="filein" value="sliding-sample_group.vcf" />
	 <param name="group" value="sliding-groups.txt" />
         <output name="fileout_snp" file="sliding-result2.snpden" />
         <output name="fileout_taj" file="sliding-result2.Tajima.D" />
         <output name="fileout_tstv" file="sliding-result2.TsTv" />
         <output name="fileout_windowed" file="sliding-result2.windowed.pi" />
	 <output name="fileout_fst" file="sliding-result2.fst.txt" />
         <output name="fileout_fst_marker" file="sliding-result2.fst.by_marker.genes.txt" />
         <output name="fileout_taj_combined" file="sliding-result2.combined.dtajima.txt" />
         <output name="fileout_windowed_combined" file="sliding-result2.combined.pi.txt" />
        </test>
	<test>
         <param name="filein" value="sample.vcf" />
         <output name="fileout_snp" file="sliding-result.snpden" />
         <output name="fileout_taj" file="sliding-result.Tajima.D" />
         <output name="fileout_tstv" file="sliding-result.TsTv" />
         <output name="fileout_windowed" file="sliding-result.windowed.pi" />
        </test>
    </tests>
    
    <!-- [OPTIONAL] Help displayed in Galaxy -->
    <help>