comparison maystro_workflow_1.xml @ 1:8bc9c1fb79f1 draft default tip

planemo upload for repository https://github.com/brsynth/galaxytools/tree/main/tools/parameters_maystro commit 98d5e65b8008dbca117b2e0655cfdd54655fac48-dirty

0:be08b189b32d

    <command detect_errors="exit_code"><![CDATA[
    #if $user_json and str($user_json) != 'None':
        cp '$user_json' '$output_json'
    #else
        python3 -c "import json; params = {
        'assembly_plan_name': '$assembly_plan_name',
        'topology': '$topology',
        'enzyme': '$enzyme',
        'execution': '$execution',
        'db_uri': '$db_uri',

        }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json'
    #end if
    && echo DEBG && cat '$output_json'
    ]]></command>
    <inputs>
        <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
            <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
            <option value="GibsonAssembly">Gibson_assembly</option>
            <option value="BASICAssembly">BASIC_assembly</option>
            <option value="BioBrickStandardAssembly">biobrick_assembly</option>

    <outputs>
        <data name="output_json" format="json" label="Workflow-1 Parameters"/>
    </outputs>
    <tests>
        <!--manual parameters set-->
        <test> 
            <param name="assembly_plan_name" value="Type2sRestrictionAssembly" />
            <param name="topology" value='circular'/>
            <param name="enzyme" value="auto"/>
            <param name="execution" value="true" />
            <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />

            <param name="fragment_column" value="fragment" />
            <param name="sequence_column" value="sequence" />
            <param name="annotation_column" value="annotation" />
            <output name="output_json">
                <assert_contents>
                    <has_n_lines n="11" />
                </assert_contents>
            </output>
        </test>
        <!--JSON parameters set-->
        <test> 
            <param name="user_json" value='test-JSON_workflow1.json'/>
            <output name="output_json">
                <assert_contents>
                    <has_n_lines n="11" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

1:8bc9c1fb79f1

    <command detect_errors="exit_code"><![CDATA[
    #if $user_json and str($user_json) != 'None':
        cp '$user_json' '$output_json'
    #else
        python3 -c "import json; params = {
        'avoid_patterns': '$avoid_patterns',
        'hairpin_constraints': '$hairpin_constraints',
        'gc_constraints': '$gc_constraints',
        'kmer_size': '$kmer_size',
        'assembly_plan_name': '$assembly_plan_name',
        'topology': '$topology',
        'enzyme': '$enzyme',
        'execution': '$execution',
        'db_uri': '$db_uri',

        }; f = open('$output_json', 'w'); json.dump(params, f, indent=4); f.close()" && echo DEBG && cat '$output_json'
    #end if
    && echo DEBG && cat '$output_json'
    ]]></command>
    <inputs>
        <param name="avoid_patterns" type="text" area="true" optional="true" label="Avoid Patterns (one per line)" />
        <param name="hairpin_constraints" type="text" area="true" label="Hairpins Constraints" optional="true" help="e.g. (you can add others Hairpins Constraints on a new line): stem_size=20, hairpin_window=200"/>
        <param name="gc_constraints" type="text" area="true" label="Enforce GC Content Constraints" optional="true" help="e.g. (you can add others Enforce GC Content Constraints on a new line): mini=0.3, maxi=0.7, window=100"/>
        <param name="kmer_size" type="integer" label="K-mer Uniqueness Size" value="" optional="true" help="e.g.: 15"/>
        <param name="assembly_plan_name" type="select" label="Assembly Calss" help="select the assambly class">
            <option value="Type2sRestrictionAssembly" selected="True">GoldenGate_assembly</option>
            <option value="GibsonAssembly">Gibson_assembly</option>
            <option value="BASICAssembly">BASIC_assembly</option>
            <option value="BioBrickStandardAssembly">biobrick_assembly</option>

    <outputs>
        <data name="output_json" format="json" label="Workflow-1 Parameters"/>
    </outputs>
    <tests>
        <!--manual parameters set-->
        <test>
            <param name="avoid_patterns" value="BsaI_site
            BsmBI_site
            BbsI_site
            SapI_site
            8x1mer
            5x3mer
            9x2mer" />
            <param name="hairpin_constraints" value='stem_size=20, hairpin_window=200'/>
            <param name="gc_constraints" value="mini=0.3, maxi=0.7, window=100
            mini=0.1, maxi=0.9, window=100"/>
            <param name="kmer_size" value="15" />
            <param name="assembly_plan_name" value="Type2sRestrictionAssembly" />
            <param name="topology" value='circular'/>
            <param name="enzyme" value="auto"/>
            <param name="execution" value="true" />
            <param name="db_uri" value="postgresql://postgres:RK17@localhost:5432/test_fragments_db" />

            <param name="fragment_column" value="fragment" />
            <param name="sequence_column" value="sequence" />
            <param name="annotation_column" value="annotation" />
            <output name="output_json">
                <assert_contents>
                    <has_n_lines n="15" />
                </assert_contents>
            </output>
        </test>
        <!--JSON parameters set-->
        <test> 
            <param name="user_json" value='test-JSON_workflow1.json'/>
            <output name="output_json">
                <assert_contents>
                    <has_n_lines n="15" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[