view dot2ct.xml @ 0:07b6202d71e2 draft default tip

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/dot2ct commit 1973f3035c10db80883d80847ea254289f5cce2a-dirty

<?xml version="1.0" encoding="UTF-8"?>
<tool id="rnastructure_dot2ct" name="Dot-Bracket to Connect Table (CT)" version="5.7.a">
    <description>Converts the first sequence in a Dot-Bracket file into a CT file</description>
    <requirements>
        <requirement type="package" version="5.7">rnastructure</requirement>
    </requirements>
    
    <version_command>dot2ct --version | grep -i version</version_command>
    
    <command>
        dot2ct
            $dotbracket_structure
            $ct_structure
    </command>
    
    <inputs>
        <param format="dbn" name="dotbracket_structure" type="data" label="Alignment in BAM or SAM format" />
    </inputs>
    
    <outputs>
        <data format="txt" name="ct_structure" label="${tool.name} on ${dotbracket_structure.name}" />
    </outputs>
    
    <tests>
        <test>
            <param name="dotbracket_structure" value="example1_input.dot-bracket.txt" format="dbn" />
            
            <output name="ct_structure" file="example1_output_seq1.ct.txt" />     
        </test>
    </tests>
    
    <help>Convert a Dot-Bracket file into a Connect Table.</help>
    
    <citations>
        <citation type="doi">10.1186/1471-2105-11-129</citation>
    </citations>
</tool>