Mercurial > repos > brigidar > vcf_to_snp

changeset 3:a928631d8297 draft

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new wrapper
author brigidar
date Mon, 02 Nov 2015 19:31:03 -0500
parents ea2f686dfd4a
children 866cd9ce1cbd
files vcf_to_snp.xml
diffstat 1 files changed, 3 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/vcf_to_snp.xml	Mon Nov 02 19:30:43 2015 -0500
+++ b/vcf_to_snp.xml	Mon Nov 02 19:31:03 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="vcf_snp" name="vcf to snp" version="0.1">
+<tool id="vcf_snp" name="vcf to snp" version="0.2">
     <description>vcf to snp for fasta</description>
     <requirements>
        <!-- Should just use the filter snp that's installed in the path -->
@@ -12,11 +12,7 @@
     <command interpreter="python">
         vcf_snp.py
         -s ${vcf}
-        -o output.txt;
-        cut -f1 output.txt > header.txt | cut -f2- output.txt > seq.txt;
-        cat seq.txt | sed 's/[[:blank:]]//g' >seq2.txt;
-        paste header.txt seq2.txt >tab.txt;
-       
+        -o output.txt
         
     </command>
 
@@ -40,7 +36,7 @@
 
 **What it does**
 
-Transforms a vcf into a snp tab file
+Transforms a vcf into a snp tab file. Has to take the nucleotide from the reference column when identical.
 
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