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Added wrapper script for correct stderr handling
author geert-vandeweyer
date Thu, 10 Apr 2014 09:44:09 -0400
parents f2d331bf3d38
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1 <tool id="BCF Tools Index" name="BCF Tools Index">
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2 <description>This tool allows the user to index sorted BCF for random access.</description>
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3
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4 <requirements>
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5 <requirement type="package" version="0.1.18">samtools</requirement>
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6 </requirements>
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8 <command interpreter='python' >bcftools_wrapper.py bcftools index $input > $output </command>
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10 <inputs>
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11 <param name="input" type="data" format="bcf" label="BCF File"/>
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12 </inputs>
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13
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14 <outputs>
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15 <data format="bcf" name="output" label= "BCF index output"/>
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16 </outputs>
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17
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18 <help>
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19 **What it does:**
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20
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21 This tool allows the user to index sorted BCF for random access using BCFtools index from the SAMtools set of utilities:
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22
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23 http://samtools.sourceforge.net/samtools.shtml#4
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25 ------
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26
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27 **Citation:**
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28
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29 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;`_
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32 If you use this tool within Galaxy, please cite `Gregory Minevich, Danny S. Park, Daniel Blankenberg, Richard J. Poole, and Oliver Hobert. CloudMap: A Cloud-based Pipeline for Analysis of Mutant Genome Sequences. (Genetics 2012 In Press)`__
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33
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34 .. __: http://biochemistry.hs.columbia.edu/labs/hobert/literature.html
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35
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36 Correspondence to gm2123@columbia.edu (G.M.) or or38@columbia.edu (O.H.)
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37
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38 </help>
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40 </tool>