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comparison samtools_faidx.xml @ 18:44265821f01f draft

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author wrtz
date Thu, 14 Jan 2016 17:51:41 -0500
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17:c34371f08c6f 18:44265821f01f
1 <tool id="samtools_faidx" name="Faidx (SAMtools)" version="1.0.0">
2 <description>Index FASTA file using samtools faidx command</description>
3 <command>
4 ln -s -f $input faidx_in.${input.ext} &amp;&amp;
5
6 samtools faidx
7
8 faidx_in.${input.ext} &amp;&amp;
9 cp faidx_in.${input.ext}.fai $output
10 </command>
11 <inputs>
12 <param name="input" type="data" label="FASTA input file" />
13 </inputs>
14 <outputs>
15 <data name="output" label="${tool.name} on ${on_string}" />
16 </outputs>
17 <help>
18 **About this tool**
19
20 **Samtools faidx**: Index reference sequence in the FASTA format or extract subsequence from indexed reference sequence. Outputs index of input file.
21
22 More info here: http://www.htslib.org/doc/samtools.html
23 </help>
24 </tool>