<tool id="RemoveSNPs" name="Remove Mismatches (SNPs) from SAM Alignment file" version="0.1.0">
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        bash $__tool_directory__/RemoveSNPs "$input1" 3 > "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="SAM alignment files" format="sam" />
	<param type="integer" name="SNPs/ mismatches allowed" value="3" />
    </inputs>
    <outputs>
        <data name="output1" format="sam" />
    </outputs>
    <tests>
        <test>
            <param name="input1" value="input.sam"/>
            <output name="output1" file="output.sam"/>
        </test>
    </tests>
    <help><![CDATA[
        This program will remove mismatches from sam file.\n Usage: RemoveSNPs test.sam 3
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{RemoveSNPs,
  author = {Tanwar, Deepak},
  year = {2017},
  title = {RemoveSNPs},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/dktanwar/NGS_Sperm_H3K4me3_Planemo_tools/tree/master/01_RemoveSNPs},
}</citation>
    </citations>
</tool>