comparison spring_minz.xml @ 17:c790d25086dc draft

"planemo upload commit b0ede77caf410ab69043d33a44e190054024d340-dirty"

16:16eb2acaaa20

        mkdir -p inputs &&
        #for input in $inputs
            link '${str(input)}' 'inputs/${input.element_identifier}' &&
            echo '${input.element_identifier}' >> 'input_list' &&
        #end for
        #for target in $targets
            python3 '$__tool_directory__/spring_minz.py' -m '$minscore' -t '${str(target)}' -n '${target.element_identifier}' -c '$crossreference' -x '$idx' -o '$output' -l input_list -i inputs &&
        #end for
        echo 0
    ]]></command>
    <inputs>
        <param format="txt" name="targets" type="data_collection" label="Target Profiles" help="Homology search result of target/query profiles `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="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.
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubhh-suite,
author = {Guerler, Govindarajoo, Zhang},

17:c790d25086dc

        mkdir -p inputs &&
        #for input in $inputs
            link '${str(input)}' 'inputs/${input.element_identifier}' &&
            echo '${input.element_identifier}' >> 'input_list' &&
        #end for
		mkdir -p targets &&
        #for target in $targets
            link '${str(target)}' 'targets/${target.element_identifier}' &&
            echo '${target.element_identifier}' >> 'target_list' &&
        #end for
		python3 '$__tool_directory__/spring_minz.py' -il input_list -ip inputs -tl target_list -tp targets -m '$minscore' -c '$crossreference' -x '$idx' -o '$output'
    ]]></command>
    <inputs>
        <param format="txt" name="targets" type="data_collection" label="Target Profiles" help="Homology search result of target/query profiles `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="crossreference" value="pdb70_random.txt"/>
            <output name="output" file="pdb70_result.txt"/>
        </test>
    </tests>
    <help><![CDATA[
This tool creates 3D models from HH-search/HH-blits homology results utilized by SPRING.
    ]]></help>
    <citations>
        <citation type="bibtex">
@misc{githubhh-suite,
author = {Guerler, Govindarajoo, Zhang},