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1 <tool id="mismatchRemovalSam" name="Remove Mismatches (SNPs) from SAM" 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
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5 bash $__tool_directory__/mismatchRemovalSam "$input1" 3 > "$output1"
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6 ]]></command>
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7 <inputs>
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8 <param type="data" name="input1" format="sam" />
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4
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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 /bin/sh: mismatchRemovalSam: command not found
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22
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23 ]]></help>
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24 <citations>
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25 <citation type="bibtex">
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26 @misc{github01_mismatch_removal,
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27 author = {LastTODO, FirstTODO},
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28 year = {TODO},
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29 title = {01_mismatch_removal},
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30 publisher = {GitHub},
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31 journal = {GitHub repository},
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32 url = {https://github.com/dktanwar/Galaxy_Tools/tree/master/01_mismatch_removal},
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33 }</citation>
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34 </citations>
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35 </tool>
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