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Anonymous committed 456d017

add fixmate tool

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Files changed (2)

     <tool file="samtools/pileup_interval.xml" />
     <tool file="samtools/samtools_flagstat.xml" />
     <tool file="samtools/samtools_rmdup.xml" />
+    <tool file="samtools/samtools_fixmate.xml" />
     <tool file="samtools/samtools_slice_bam.xml" />
     <tool file="samtools/samtools_sort.xml" />
     <tool file="samtools/samtools_varfilter.xml" />

tools/samtools/samtools_fixmate.xml

+<tool id="samtools_fixmate" name="samtools fixmate" version="1.0.0">
+  <requirements>
+    <requirement type="package">samtools</requirement>
+  </requirements>
+  <description>fixmate</description>
+  <command>samtools fixmate 
+  "$input1" "$output1"
+  2&gt;&amp;1 || echo "Error running samtools fixmate." &gt;&amp;2
+  </command>
+  <inputs>
+    <param name="input1" type="data" format="bam" label="BAM File" />
+  <outputs>
+    <data name="output1" format="bam" />
+  </outputs>
+  <tests>
+    <test>
+      <param name="input1" value="1.bam" ftype="bam" />
+      <output name="output1" file="1.bam" ftype="bam" sort="True"/>
+    </test>
+  </tests>
+  <help>
+
+**What it does**
+
+Fill in mate coordinates, ISIZE and mate related flags from a name-sorted alignment.
+
+------
+
+**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>