# HG changeset patch
# User biomonika
# Date 1407962046 14400
# Node ID 188b16f2d6f8fdea5d0286e51069a4df58f40a8c
# Parent  f63302fe8f0c8f6c6a6fa228fca8939c9f9eb49f
Deleted selected files

diff -r f63302fe8f0c -r 188b16f2d6f8 LINKYX_mpileup_wrapper.sh
--- a/LINKYX_mpileup_wrapper.sh	Wed Aug 13 16:33:50 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-#!/bin/bash
-results=$1;
-bam_file=$2;
-reference=$3;
-
-#samtools mpileup -uf $reference $2 >$results;
-samtools mpileup -uf $reference $2 | bcftools view -p 0.85 -cgv - | vcfutils.pl varFilter >$results
\ No newline at end of file
diff -r f63302fe8f0c -r 188b16f2d6f8 LINKYX_mpileup_wrapper.xml
--- a/LINKYX_mpileup_wrapper.xml	Wed Aug 13 16:33:50 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-<tool id="LINKYX_mpileup" name="LINKYX_mpileup">
-      <description>Run mpileup with LINKYX-specific parameters</description>
-      <command interpreter="bash">LINKYX_mpileup_wrapper.sh $output $input $input1</command>
-      <inputs>
-        <param format="bam" name="input" type="data" label="Alignment file"/>
-        <param format="fasta" name="input1" type="data" label="Reference file"/>
-      </inputs>
-      <outputs>
-        <data format="tabular" name="output" />
-      </outputs>
-  
-     <tests>
-       <test>
-        <output name="out_file1" file="alignent_mpileup.txt"/>
-       </test>
-     </tests>
-   
-     <help>
-   This tool tests if primers are present in gorilla female or on human Y or chimp Y chromosome.
-     </help>
-   
-   </tool>
\ No newline at end of file