diff vcf_to_snp.xml @ 7:b617219a70b5 draft

new option

--- a/vcf_to_snp.xml	Fri Nov 06 15:12:17 2015 -0500
+++ b/vcf_to_snp.xml	Fri Nov 06 15:17:20 2015 -0500
@@ -1,4 +1,4 @@
-<tool id="vcf_snp" name="vcf to snp" version="0.3">
+<tool id="vcf_snp" name="vcf to snp" version="0.5">
     <description>vcf to snp for fasta</description>
     <requirements>
        <!-- Should just use the filter snp that's installed in the path -->
@@ -8,21 +8,25 @@
 ## The command is a Cheetah template which allows some Python based syntax.
 ## Lines starting hash hash are comments. Galaxy will turn newlines into spaces
 ## ! We only have a simple single command here.
-
-    <command interpreter="/usr/local/anaconda/bin/python">
+    <command interpreter="python">
         vcf_snp.py
         -s ${vcf}
-        -o output.txt
+        -p ${pos}
+        -o output.txt;
+        echo ${vcf.name} > name.txt;
+        cut -f2 output.txt >seq.txt;
+        paste name.txt seq.txt> output2.txt
         
     </command>
 
     <inputs>
         <param  name="vcf" type="data" label="vcf" help=""/>
+        <param  name="pos" type="data" label="positions" help=""/>
         
     </inputs>
 
     <outputs>
-        <data format="tabular" name="output_file" label="${vcf}" from_work_dir="output.txt">
+        <data format="tabular" name="output_file" label="${vcf}" from_work_dir="output2.txt">
             </data>
     </outputs>