diff phe_samtools_mpileup.xml @ 0:3dd238a07d9b draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phe_samtools_mpileup.xml	Tue Apr 19 07:33:10 2016 -0400
@@ -0,0 +1,38 @@
+<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>
+      <requirement type="package" version="1.3">bcftools</requirement>
+  </requirements>
+  <stdio>
+    <!-- Assume anything other than zero is an error -->
+    <exit_code range="1:" />
+    <exit_code range=":-1" />
+  </stdio>
+  <command interpreter="bash">
+    phe_samtools_mpileup.sh $input_bam $ref_file $outvcf
+  </command>
+  <inputs>
+    <param name="input_bam" type="data" format="bam" label="BAM file" />
+    <param name="ref_file" type="data" format="fasta" label="Using reference file" />
+  </inputs>
+  <outputs>
+    <data format="vcf" name="outvcf" label="${tool.name} on ${on_string} VCF" />
+  </outputs>
+  <tests>
+      <test>
+        <param name="input_bam" value="in_short.bam" ftype="bam" />
+        <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>