comparison temp.xml @ 16:c613f8c96e6d draft

planemo upload for repository https://github.com/portiahollyoak/Tools commit c734ef937d8ed788fded64ed8455e7fc7b89278c

15:65ae84fc6689

<tool id ="run_TEMP" name="TEMP" version="0.1.7">
    <description></description>
    <requirements>
        <!-- The following are classical toolshed packages and should be removed
        once conda is deemed stable-->
        <requirement type="package" version="1.6.922">bioperl</requirement>

        <param name="median_insertsize" value="" type="integer" label="Median Insert Length"/>
        <param name="mismatches" min="0" max="5" type="integer" value="3" label="Allow this many mismatches when aligning to TEs"/>
        <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum score difference between optimal and suboptimal alignment to consider read uniquely mapped"/>
    </inputs>
    <outputs>
        <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertion summary file" />
        <data format="bed" type="data" name="absence_summary" label="${alignment.element_identifier} Absence summary file" />
        <data format="zip" type="data" name="archive" label="${alignment.element_identifier} Compressed output files" />
    </outputs>
    <tests>
        <test>
            <param name="alignment" value="chr2l_bwa_mem.bam" ftype="bam"/>

16:c613f8c96e6d

<tool id ="run_TEMP" name="TEMP" version="0.1.8">
    <description></description>
    <requirements>
        <!-- The following are classical toolshed packages and should be removed
        once conda is deemed stable-->
        <requirement type="package" version="1.6.922">bioperl</requirement>

        <param name="median_insertsize" value="" type="integer" label="Median Insert Length"/>
        <param name="mismatches" min="0" max="5" type="integer" value="3" label="Allow this many mismatches when aligning to TEs"/>
        <param name="minimum_score_difference" type="integer" min="10" max="37" value="30" label="Minimum score difference between optimal and suboptimal alignment to consider read uniquely mapped"/>
    </inputs>
    <outputs>
        <data format="bed" type="data" name="insertion_summary" label="${alignment.element_identifier} Insertions" />
        <data format="bed" type="data" name="absence_summary" label="${alignment.element_identifier} Absences" />
        <data format="zip" type="data" name="archive" label="${alignment.element_identifier} Compressed output files" />
    </outputs>
    <tests>
        <test>
            <param name="alignment" value="chr2l_bwa_mem.bam" ftype="bam"/>