Mercurial > repos > brigidar > snp_to_bed

diff snp_to_bed.xml @ 0:9c02f5e8e657 draft

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author brigidar
date Wed, 07 Oct 2015 15:17:51 -0400
parents
children c5195904b225
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/snp_to_bed.xml	Wed Oct 07 15:17:51 2015 -0400
@@ -0,0 +1,15 @@
+<tool id="snp_to_bed" name="snp location to bed format" version="0.1">
+    <description>removes unwanted column</description>
+    <command>
+        cat $input1 | sed '1d'| awk -F "\t" -v OFS="\t" '{print $1, $2-1, $2}'>> $out_file1  </command>
+    <inputs>
+        <param name="input1" type="data" label="input file"/>
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="input" metadata_source="input1"/>
+    </outputs>
+    <tests>
+    </tests>
+    <help>
+    </help>
+</tool>