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comparison 01_RemoveSNPs/RemoveSNPs.xml @ 4:853b0c9367b6 draft

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author dktanwar
date Mon, 16 Oct 2017 13:45:19 -0400
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1 <tool id="RemoveSNPs" name="Remove Mismatches (SNPs) from SAM Alignment file" version="0.1.0">
2 <requirements>
3 </requirements>
4 <command detect_errors="exit_code"><![CDATA[
5 bash $__tool_directory__/RemoveSNPs "$input1" 3 > "$output1"
6 ]]></command>
7 <inputs>
8 <param type="data" name="SAM alignment files" format="sam" />
9 <param type="integer" name="SNPs/ mismatches allowed" value="3" />
10 </inputs>
11 <outputs>
12 <data name="output1" format="sam" />
13 </outputs>
14 <tests>
15 <test>
16 <param name="input1" value="input.sam"/>
17 <output name="output1" file="output.sam"/>
18 </test>
19 </tests>
20 <help><![CDATA[
21 This program will remove mismatches from sam file.\n Usage: RemoveSNPs test.sam 3
22 ]]></help>
23 <citations>
24 <citation type="bibtex">
25 @misc{RemoveSNPs,
26 author = {Tanwar, Deepak},
27 year = {2017},
28 title = {RemoveSNPs},
29 publisher = {GitHub},
30 journal = {GitHub repository},
31 url = {https://github.com/dktanwar/NGS_Sperm_H3K4me3_Planemo_tools/tree/master/01_RemoveSNPs},
32 }</citation>
33 </citations>
34 </tool>