# HG changeset patch
# User biomonika
# Date 1408028619 14400
# Node ID e749df597df823c04969a417143b605002098c08
# Parent  2a0671e8cb5e74a2d5e36781c60c5aa3aa7204b0
Deleted selected files

diff -r 2a0671e8cb5e -r e749df597df8 Archive.zip
Binary file Archive.zip has changed
diff -r 2a0671e8cb5e -r e749df597df8 LINKYX_mpileup_wrapper.sh
--- a/LINKYX_mpileup_wrapper.sh	Thu Aug 14 11:03:26 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 $2 2>log.txt | bcftools view -p 0.85 -cgv - 2>>log.txt| vcfutils.pl varFilter >$results 2>>log.txt
\ No newline at end of file
diff -r 2a0671e8cb5e -r e749df597df8 LINKYX_mpileup_wrapper.xml
--- a/LINKYX_mpileup_wrapper.xml	Thu Aug 14 11:03:26 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="vcf" 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
diff -r 2a0671e8cb5e -r e749df597df8 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Aug 14 11:03:26 2014 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,23 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-    <package name="perl" version="5.18.1">
-        <repository changeset_revision="a1a111b9faa5" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
-    </package>
-    <package name="bioperl" version="1.6.922">
-        <install version="1.0">
-            <actions>
-                <action type="setup_perl_environment">
-                    <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="perl" version="5.18.1" />
-                    </repository>
-                   <!-- allow downloading and installing an Perl package from cpan.org-->
-                   <package>Bio::DB::Sam</package>
-                   <package>http://search.cpan.org/CPAN/authors/id/L/LD/LDS/Bio-SamTools-1.39.tar.gz</package>
-                </action>
-            </actions>
-        </install>
-        <readme>
-            Bundle::BioPerl
-        </readme>
-    </package>
-</tool_dependency>