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