comparison intarna.xml @ 6:3f6715821198 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/rna_tools/intarna commit da73dae857c2ee9447aad05f260f7da5ea1db3a6

5:233dfabc8592

<tool id="intarna" name="IntaRNA" version="2.1.0.2">
    <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
    <macros>
        <macro name="query_macro">
            <param name="_query" argument="--query" format="fasta" type="data" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" />
            <conditional name="qAcc_cond">

                label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>
            <param argument="--tAccL" type="integer" value="100" min="0" max="99999"
                label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'tAccW'"/>
        </macro>
        <macro name="seed_macro">
            <param argument="--noSeed" truevalue="--noSeed" falsevalue="" checked="False" type="boolean"
                label="Disable seed constraint entirely for computation" help=""/>
            <param argument="--seedBP" type="integer" value="7" min="2" max="20"  label="Min. number of basepairs in seed" help="number of inter-molecular base pairs within the seed region"/>
            <param argument="--seedMaxUP" type="integer" value="0" min="0" max="20"
                label="Max. overall number of unpaired bases (query+target)" help=""/>
        </macro>

                <option value="B">in both sequences</option>
            </param>
        </macro>
    </macros>
    <requirements>
        <requirement type="package" version="2.1.0">intarna</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
    </stdio>

6:3f6715821198

<tool id="intarna" name="IntaRNA" version="2.2.0">
    <description>Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites.</description>
    <macros>
        <macro name="query_macro">
            <param name="_query" argument="--query" format="fasta" type="data" label="Query sequence(s)" help="Sequences have to use IUPAC nucleotide encoding. File must be in FASTA format" />
            <conditional name="qAcc_cond">

                label="Max. interaction length" help="... for query accessibility computation. Set to 0 to use full sequence length"/>
            <param argument="--tAccL" type="integer" value="100" min="0" max="99999"
                label="Max. loop length" help="... for query accessibility computation. 0 defaults to sliding window size 'tAccW'"/>
        </macro>
        <macro name="seed_macro">
            <param argument="--noSeed" truevalue="--noSeed" falsevalue="" checked="false" type="boolean"
                label="Disable seed constraint entirely for computation" help=""/>
            <param argument="--seedBP" type="integer" value="7" min="2" max="20"  label="Min. number of basepairs in seed" help="number of inter-molecular base pairs within the seed region"/>
            <param argument="--seedMaxUP" type="integer" value="0" min="0" max="20"
                label="Max. overall number of unpaired bases (query+target)" help=""/>
        </macro>

                <option value="B">in both sequences</option>
            </param>
        </macro>
    </macros>
    <requirements>
        <requirement type="package" version="2.2.0">intarna</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
        <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
    </stdio>