comparison spring_minz.xml @ 29:41353488926c draft

"planemo upload commit 1c0a60f98e36bccb6d6c85ff82a8d737a811b4d5"

28:75d1aedc9b3f

<tool id="spring_minz" name="SPRING min-Z" version="0.1.2" python_template_version="3.5">
    <description>filter operation</description>
    <code file="spring_minz.py"/>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p targets &&
        #for target in $targets
            link '${str(target)}' 'targets/${target.element_identifier}' &&
            echo '${target.element_identifier}' >> 'target_list' &&

                <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input profiles" help="Homology search results of input profiles `hhr`."/>
            </when>
        </conditional>
        <param format="tabular" 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="Score threshold" value="10" min="1" max="200" 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="20" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="SPRING min-Z Table"/>
        <data format="txt" name="log" label="SPRING min-Z Log" />
    </outputs>

29:41353488926c

<tool id="spring_minz" name="SPRING min-Z" version="0.1.2" python_template_version="3.5">
    <description>filter operation</description>
    <command detect_errors="exit_code"><![CDATA[
        mkdir -p targets &&
        #for target in $targets
            link '${str(target)}' 'targets/${target.element_identifier}' &&
            echo '${target.element_identifier}' >> 'target_list' &&

                <param format="txt" name="inputs" type="data_collection" collection_type="list" label="Input profiles" help="Homology search results of input profiles `hhr`."/>
            </when>
        </conditional>
        <param format="tabular" 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="Score threshold" value="10" min="1" max="200" 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="20" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="SPRING min-Z Table"/>
        <data format="txt" name="log" label="SPRING min-Z Log" />
    </outputs>