comparison hyphy_conv.xml @ 2:f6e7b5955712 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"

1:c1d24ff838c8

        hyphy conv
            '$gencodeid'
            '$deletions'
            conv_input.fa
            aa.nex
            > ./conv.log
        @ERRORS@
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fasta" label="Input codon alignment"/>
        <param name="save_log" type="boolean" truevalue="Yes" falsevalue="No" checked="false" label="Save the conversion log to your history" />
        <expand macro="gencode"/>
        <param name="deletions" type="boolean" truevalue="Keep Deletions" falsevalue="Skip Deletions" label="Keep deletions" help="If this is checked, deletions will be left in the output file"/>
    </inputs>
    <outputs>
        <data name="conv_log" format="txt" from_work_dir="conv.log">
            <filter>save_log</filter>
        </data>
        <data name="proteins" format="nex" from_work_dir="aa.nex" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="conv-in1.fa"/>

2:f6e7b5955712

        hyphy conv
            '$gencodeid'
            '$deletions'
            conv_input.fa
            aa.nex
        @ERRORS@
    ]]></command>
    <inputs>
        <param name="input_file" type="data" format="fasta" label="Input codon alignment"/>
        <expand macro="gencode"/>
        <param name="deletions" type="boolean" truevalue="Keep Deletions" falsevalue="Skip Deletions" label="Keep deletions" help="If this is checked, deletions will be left in the output file"/>
    </inputs>
    <outputs>
        <data name="proteins" format="nex" from_work_dir="aa.nex" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="fasta" value="conv-in1.fa"/>