diff vcftools_isec.xml @ 0:799feac145c8 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/vcftools_isec.xml	Sun Nov 24 11:12:03 2013 -0500
@@ -0,0 +1,63 @@
+<tool id="vcftools_isec" name="Intersect" version="0.1">
+    <description>multiple VCF datasets</description>
+
+    <requirements>
+        <requirement type="package">tabix</requirement>
+        <requirement type="package" version="0.1.11">vcftools</requirement>
+    </requirements>
+    
+    <command>
+        ## Preprocessing for each dataset.
+        #set dataset_names = []
+        #for i, $input in enumerate( $inputs ):
+            ## Sort file.
+            vcf-sort ${input.file} > ${i}.vcf.sorted ;
+
+            ## Compress.
+            bgzip ${i}.vcf.sorted ;
+
+            ## Index.
+            tabix -p vcf ${i}.vcf.sorted.gz ;
+
+            #silent dataset_names.append( str($i) + '.vcf.sorted.gz' )
+        #end for
+
+        ## Intersect.
+        vcf-isec -f
+        #if $complement:
+        -c
+        #end if 
+        #echo ' '.join( dataset_names ) # > ${output}
+    </command>
+    <inputs>
+        <repeat name="inputs" title="Dataset" min="2">
+            <param name="file" label="Dataset" type="data" format="vcf"/>
+        </repeat>
+        <param name="complement" type="boolean" label="Complement intersection" help="If checked, output positions present in the first file but missing from the other files"/>
+    </inputs>
+
+    <outputs>
+        <data name="output" format="vcf"/>
+    </outputs>
+
+    <stdio>
+        <regex match=".*" source="both" level="log" description="tool progress"/>
+    </stdio>
+
+    <tests>
+        <!-- Cannot specify multiple repeats in test framework right now.
+        <test>
+            <param name='inputs|1' value='1.vcf' />
+            <param name='inputs|2' value='2.vcf' />
+            <param name='complement' value='False' />
+            <output name='output' file='out.vcf' />
+        </test>
+        -->
+    </tests>
+
+    <help>
+        Please see the VCFtools `documentation`__ for help and further information.
+
+        .. __: http://vcftools.sourceforge.net/docs.html
+    </help>
+</tool>