| Previous changeset 1:59eca98715b4 (2015-12-21) Next changeset 3:65b5406977c9 (2015-12-21) |
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Commit message:
Deleted selected files |
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removed:
phe_samtools_mpileup.sh phe_samtools_mpileup.xml |
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| 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 |
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| @@ -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 |
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| 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 |
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| @@ -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. <http://www.ncbi.nlm.nih.gov/pubmed/19505943>`_ - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - - </help> -</tool> |