comparison spring_minz.xml @ 9:4ac5d5a9b21c draft

"planemo upload commit f465445ebca0307953f59938494a2244ca8ea23c"

8:f2f38991c36f

        mkdir -p inputs &&
        #for input in $inputs
            link '${str(input)}' 'inputs/${input.element_identifier}' &&
            echo '${input.element_identifier}' >> 'input_list' &&
        #end for
        python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -o '$output' -l input_list -i inputs
    ]]></command>
    <inputs>
        <param format="txt" name="target" type="data" label="Target Profile" help="Homology search result of target/query profile `hhr`."/>
        <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/>
        <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins pairs from SPRING database protocol."/>
        <param name="minscore" type="integer" label="min-Z score threshold" value="10" min="1" max="100" help="Matching interaction pairs with a score lower than this threshold will be excluded."/>
    </inputs>
    <outputs>
        <data format="txt" name="output" />
    </outputs>
    <tests>

9:4ac5d5a9b21c

        mkdir -p inputs &&
        #for input in $inputs
            link '${str(input)}' 'inputs/${input.element_identifier}' &&
            echo '${input.element_identifier}' >> 'input_list' &&
        #end for
        python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '$target' -c '$crossreference' -x '$idx' -o '$output' -l input_list -i inputs
    ]]></command>
    <inputs>
        <param format="txt" name="target" type="data" label="Target Profile" help="Homology search result of target/query profile `hhr`."/>
        <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input Profiles" help="Homology search results of input profiles `hhr`."/>
        <param format="txt" name="crossreference" type="data" label="Cross Reference" help="Cross reference of interacting proteins `first_id metadata_id second_id`."/>
        <param name="minscore" type="integer" label="min-Z score threshold" value="10" min="1" max="100" help="Matching interaction pairs with a score lower than this threshold will be excluded."/>
        <param name="idx" type="integer" label="Identifier length" value="6" min="1" max="10" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/>
    </inputs>
    <outputs>
        <data format="txt" name="output" />
    </outputs>
    <tests>