Mercurial > repos > biomonika > monika_mpileup
changeset 21:e749df597df8 draft
Deleted selected files
author | biomonika |
---|---|
date | Thu, 14 Aug 2014 11:03:39 -0400 |
parents | 2a0671e8cb5e |
children | 6e7041bf4c99 |
files | Archive.zip LINKYX_mpileup_wrapper.sh LINKYX_mpileup_wrapper.xml tool_dependencies.xml |
diffstat | 4 files changed, 0 insertions(+), 52 deletions(-) [+] |
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--- 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
--- 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
--- 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>