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view mismatchRemovalSam.xml @ 2:631ceebd8d16 draft

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author dktanwar
date Mon, 16 Oct 2017 10:20:56 -0400
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<tool id="mismatchRemovalSam" name="Remove Mismatches (SNPs) from SAM" version="0.1.0">
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        mismatchRemovalSam "$input1" 3 > "$output1"
    ]]></command>
    <inputs>
        <param type="data" name="input1" 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[
        /bin/sh: mismatchRemovalSam: command not found

    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{github01_mismatch_removal,
  author = {LastTODO, FirstTODO},
  year = {TODO},
  title = {01_mismatch_removal},
  publisher = {GitHub},
  journal = {GitHub repository},
  url = {https://github.com/dktanwar/Galaxy_Tools/tree/master/01_mismatch_removal},
}</citation>
    </citations>
</tool>