# HG changeset patch
# User ulfschaefer
# Date 1450700568 18000
# Node ID 7ec666e2f315d3b69d960931ab321666f31945cd
# Parent  59eca98715b4418a49f940a1149c1124769a3442
Deleted selected files

diff -r 59eca98715b4 -r 7ec666e2f315 phe_samtools_mpileup.sh
--- a/phe_samtools_mpileup.sh	Mon Dec 21 07:22:34 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,22 +0,0 @@
-#!/bin/bash
-
-echo $@
-
-SAM=$1
-shift
-REF=$1
-shift
-OUTVCF=$1
-
-TMPBAM=$$.tmpbam
-TMPBAM2=$$.tmpbam2
-
-samtools view -bS $SAM > $TMPBAM
-samtools sort $TMPBAM $TMPBAM2
-
-CMD="samtools mpileup -t DP,DV,DP4,DPR,SP -Auf $REF $TMPBAM2.bam | bcftools call -m -f GQ > $OUTVCF"
-
-echo "CMD: "$CMD
-eval $CMD
-rm $TMPBAM
-rm $TMPBAM2.bam
diff -r 59eca98715b4 -r 7ec666e2f315 phe_samtools_mpileup.xml
--- a/phe_samtools_mpileup.xml	Mon Dec 21 07:22:34 2015 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,32 +0,0 @@
-<tool id="phe_samtools_mpileup" name="PHE MPileup" version="1.0">
-  <description>PHE SNP and indel caller</description>
-  <requirements>
-      <requirement type="package" version="1.1">samtools</requirement>
-  </requirements>
-  <command interpreter="bash">
-    phe_samtools_mpileup.sh $input_sam $ref_file $outvcf
-  </command>
-  <inputs>
-    <param name="input_sam" type="data" format="sam" label="SAM file" />
-    <param name="ref_file" type="data" format="fasta" label="Using reference file" />
-  </inputs>
-  <outputs>
-    <data format="vcf" name="outvcf" label="${tool.name} on ${on_string} VCF" />
-  </outputs>
-  <tests>
-      <test>
-        <param name="in_sam" value="in_short.sam" ftype="sam" />
-        <param name="ref_file" value="ref.fa" ftype="fasta" />
-        <output name="outvcf" file="out.vcf" ftype="vcf" />
-      </test>
-  </tests>
-  <help>
-
-**Citation**
-
-For the underlying tool, please cite `Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9. &lt;http://www.ncbi.nlm.nih.gov/pubmed/19505943&gt;`_
-
-If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.*
-
-  </help>
-</tool>