comparison chira_extract.xml @ 11:a618f28e1496 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/chira commit 51f68a6d51d9e87f8e54021ce760b1506a3589b8"

10:7ec1d063fecd

            -f1 '$reference.ref_fasta1'
            -f2 '$reference.ref_fasta2'
        #end if
        $hybridize
        $seed_interaction
        $summarize
        -a '$accessibility'
        -m '$intarna_mode'
        -p "\${GALAXY_SLOTS:-2}"
        -o ./
    ]]></command>

    <inputs>

            </when>
        </conditional>
        <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"
               label="Hybridize chimeric loci?"
               help="Turning this option on increases the run time of the tool significantly."/>
        <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--noSeed" checked="false"
               label="Enforce seed interaction?"/>
        <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
               label="Compute accessibility profiles for interacting sequences?"/>
        <param name="intarna_mode" type="select">
            <option value="H">Heuristic</option>
            <option value="M">Exact</option>
            <option value="S">Seed-only</option>
        </param>
        <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"
               label="Summarize interactions at loci level?"/>
    </inputs>

    <outputs>
        <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/>
        <data format="tabular" name="singletons" from_work_dir="singletons" label="ChiRA singleton reads on ${on_string}"/>
        <data format="tabular" name="interactions" from_work_dir="interactions" label="ChiRA interaction summary on ${on_string}">
            <filter>summarize == True</filter>
        </data>
    </outputs>

    <tests>
        <test expect_num_outputs="3">
            <param name="loci" value="loci.counts"/>
            <param name="ref_type" value="split"/>
            <param name="ref_fasta1" value="ref1.fasta"/>
            <param name="ref_fasta2" value="ref2.fasta"/>
            <param name="annot_choice" value="no"/>
            <param name="hybridize" value="true" />
            <param name="summarize" value="true" />
            <output name="chimeras" file="chimeras"/>
            <output name="singletons" file="singletons"/>
            <output name="interactions" file="interactions"/>
        </test>
    </tests>
    <help>

11:a618f28e1496

            -f1 '$reference.ref_fasta1'
            -f2 '$reference.ref_fasta2'
        #end if
        $hybridize
        $seed_interaction
        -sbp '$seed_bp'
        -smpu '$seed_min_pu'
        -acc '$accessibility'
        -accw '$acc_width'
        -m '$intarna_mode'
        $summarize
        -p "\${GALAXY_SLOTS:-2}"
        -o ./
    ]]></command>

    <inputs>

            </when>
        </conditional>
        <param name="hybridize" type="boolean" truevalue="-r" falsevalue="" checked="false"
               label="Hybridize chimeric loci?"
               help="Turning this option on increases the run time of the tool significantly."/>
        <param name="intarna_mode" type="select">
            <option value="H">Heuristic</option>
            <option value="M">Exact</option>
            <option value="S">Seed-only</option>
        </param>
        <param name="seed_interaction" type="boolean" truevalue="" falsevalue="--noSeed" checked="true"
               label="Enforce seed interaction?"/>
        <param name="seed_bp" type="integer" value="5" min="2" max="20"
               label="Number of inter-molecular base pairs within the seed region"
               help="IntaRNA --seedBP parameter"/>
        <param name="seed_min_pu" type="float" value="0" min="0" max="1"
               label="Minimal unpaired probability (per sequence) a seed region may have"
               help="IntaRNA --seedMinPu parameter"/>
        <param name="accessibility" type="boolean" truevalue="C" falsevalue="N" checked="false"
               label="Compute accessibility profiles for interacting sequences?"/>
        <param name="acc_width" type="integer" value="150" min="0" max="99999"
               label="Sliding window size for accessibility computation"
               help="IntaRNA --accW parameter"/>
        <param name="temperature" type="float" value="37" min="0" max="100"
               label="IntaRNA temperature parameter in Celsius to setup the VRNA energy parameters"/>
        <param name="summarize" type="boolean" truevalue="-s" falsevalue="" checked="false"
               label="Summarize interactions at loci level?"/>
    </inputs>

    <outputs>
        <data format="tabular" name="chimeras" from_work_dir="chimeras" label="ChiRA chimeric reads on ${on_string}"/>
        <data format="tabular" name="interactions" from_work_dir="interactions" label="ChiRA interaction summary on ${on_string}">
            <filter>summarize == True</filter>
        </data>
    </outputs>

    <tests>
        <test expect_num_outputs="2">
            <param name="loci" value="loci.counts"/>
            <param name="ref_type" value="split"/>
            <param name="ref_fasta1" value="ref1.fasta"/>
            <param name="ref_fasta2" value="ref2.fasta"/>
            <param name="annot_choice" value="no"/>
            <param name="hybridize" value="true" />
            <param name="summarize" value="true" />
            <output name="chimeras" file="chimeras"/>
            <output name="interactions" file="interactions"/>
        </test>
    </tests>
    <help>