view combine_bracken_outputs.xml @ 0:6e90a30b214f draft default tip

planemo upload for repository https://github.com/youyuh48/galaxy-tools/tree/master/tools/combine_bracken_outputs commit e6c33bbc6689e9a0a12ff3f915515d894f1b4671-dirty

<tool id="combine_bracken_outputs" name="Combine Bracken Outputs" version="0.1.0+galaxy0" profile="19.01">
    <requirements>
        <requirement type="package" version="2.7">bracken</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#set dataset_names = []
#for $report in $reports
    #silent dataset_names.append(str($report.element_identifier))
#end for

combine_bracken_outputs.py
--names "${",".join($dataset_names)}"
--files
#for $report in $reports 
    '$report'
#end for
--output '$output'
    ]]></command>
    <inputs>
        <param name="reports" label="Bracken report files" type="data" format="tabular" min="2" multiple="True"/>
    </inputs>
    <outputs>
        <data name="output" format="tabular" label="Combined Bracken report file"/>
    </outputs>
    <citations>
        <citation type="bibtex">
            title = {combine_bracken_outputs},
            publisher = {GitHub},
            journal = {GitHub repository},
            url = {https://github.com/jenniferlu717/Bracken}
        </citation>
    </citations>
</tool>