comparison spring_minz.xml @ 10:860bd6f8f480 draft

"planemo upload commit 4b670114bbbbbe3c5207cee572a20dc48f27494a"

9:4ac5d5a9b21c

    <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>
        <test>
            <param name="target" value="NP_000282.1.hhr"/>
            <param name="inputs">
                <collection type="list">
                    <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
                    <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" />
                    <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" />
                    <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" />
                </collection>
            </param>
            <param name="crossreference" value="index.txt"/>
            <output name="output" file="result.txt"/>
        </test>
    </tests>
    <help><![CDATA[
This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING. Putative interactions are identified by
evaluating the min-Z score. The min-Z is the smaller of the two Z-scores for a pair of sequences matching an existing protein-protein complex structure.

10:860bd6f8f480

    <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="20" help="Specify the length of the identifier e.g. `1ACB_A` has length 6."/>
    </inputs>
    <outputs>
        <data format="txt" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="target" value="7BQY_A.hhr"/>
            <param name="idx" value="10"/>
            <param name="inputs">
                <collection type="list">
                    <element name="6W37_A.hhr" value="6W37_A.hhr" />
                    <element name="6W4H_A.hhr" value="6W4H_A.hhr" />
                    <element name="6W4H_B.hhr" value="6W4H_B.hhr" />
                    <element name="6W9C_A.hhr" value="6W9C_A.hhr" />
                    <element name="6W9Q_A.hhr" value="6W9Q_A.hhr" />
                    <element name="6WEY_A.hhr" value="6WEY_A.hhr" />
                    <element name="6WJI_A.hhr" value="6WJI_A.hhr" />
                    <element name="6WLC_A.hhr" value="6WLC_A.hhr" />
                </collection>
            </param>
            <param name="crossreference" value="dbCAN_random.txt"/>
            <output name="output" file="dbCAN_result.txt"/>
        </test>
        <test>
            <param name="target" value="NP_000282.1.hhr"/>
            <param name="inputs">
                <collection type="list">
                    <element name="NP_000282.1.hhr" value="NP_000282.1.hhr" />
                    <element name="NP_000290.2.hhr" value="NP_000290.2.hhr" />
                    <element name="NP_000548.2.hhr" value="NP_000548.2.hhr" />
                    <element name="NP_000836.2.hhr" value="NP_000836.2.hhr" />
                </collection>
            </param>
            <param name="crossreference" value="pdb70_random.txt"/>
            <output name="output" file="pdb70_result.txt"/>
        </test>
    </tests>
    <help><![CDATA[
This tool filters HH-search/HH-blits homology results through the protein interaction cross reference generated by SPRING. Putative interactions are identified by
evaluating the min-Z score. The min-Z is the smaller of the two Z-scores for a pair of sequences matching an existing protein-protein complex structure.