Mercurial > repos > biomonika > monika_mpileup
changeset 10:188b16f2d6f8 draft
Deleted selected files
| author | biomonika |
|---|---|
| date | Wed, 13 Aug 2014 16:34:06 -0400 |
| parents | f63302fe8f0c |
| children | 6351a3faf4e3 |
| files | LINKYX_mpileup_wrapper.sh LINKYX_mpileup_wrapper.xml |
| diffstat | 2 files changed, 0 insertions(+), 29 deletions(-) [+] |
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--- 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
--- 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