comparison selenzy_wrapper.xml @ 3:be121e7d0c9d draft default tip

planemo upload for repository https://github.com/brsynth/selenzy-wrapper commit 45a7c182f39c67507b05e39509b865a04ecdd1f9

2:164ccfcd18ec

    <command detect_errors="exit_code"><![CDATA[
        python -m selenzy_wrapper '$pathway' '$uniprot_ids'
        --nb_targets '$adv.nb_targets'
        --d '$adv.direction'
        $adv.NoMSA
        --host_taxID '$adv.host_taxID'
        #if str($adv.enzyme_taxIDs) != "":
            --enzyme_taxIDs '$adv.enzyme_taxIDs'
        #end if
        --nb_ids '$adv.nb_ids'
        --to_csv '$uniprot_ids_csv'
        --data-path "\${TMPDIR:-.}"
    ]]></command>
    <inputs>
        <param name="pathway" type="data" format="sbml" label="Pathway (SBML)" />
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="host_taxID" type="integer" value="83333" label="Host taxon ID" help="Taxon ID of the chassis (default: 83333 [E. coli K12])" />
            <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
            <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" help=" Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]" />
            <param name="nb_targets" type="integer" value="500" min="1" label="Number of targets to display in results" help="Number of targets to display in results (before taxon IDs filtering) [default = 500]" />
            <param name="direction" type="float" value="0" label="Use similarity values for preferred reaction direction only" help="You can choose to rank similarities in both reaction directions or to use only the direction of the reaction based on a consensus list that has been generated according to reaction information based on curated information from MetaCyc (Metabolic Pathway Database) [default=0 (OFF)]" />
            <param argument="--NoMSA" type="boolean" falsevalue="--NoMSA" truevalue="" checked="true" display="checkboxes" label="Do not compute MSA/conservation scores ?" help="Do not compute Multiple Sequence Alignment and conservation scores ? (MSA scores are computed by default)" />

3:be121e7d0c9d

    <command detect_errors="exit_code"><![CDATA[
        python -m selenzy_wrapper '$pathway' '$uniprot_ids'
        --nb_targets '$adv.nb_targets'
        --d '$adv.direction'
        $adv.NoMSA
        #if str($host_taxID_type_conditional.host_taxID_type) == "tsv":
            --host_taxID `sed 1d ${host_taxID_type_conditional.host_taxID_file}`
        #else:
            --host_taxID '$host_taxID_type_conditional.host_taxID_int'
        #end if
        #if str($adv.enzyme_taxIDs) != "":
            --enzyme_taxIDs '$adv.enzyme_taxIDs'
        #end if
        --nb_ids '$adv.nb_ids'
        --to_csv '$uniprot_ids_csv'
        --data-path "\${TMPDIR:-.}"
    ]]></command>
    <inputs>
        <param name="pathway" type="data" format="sbml" label="Pathway (SBML)" />
        <conditional name="host_taxID_type_conditional">
            <param name="host_taxID_type" type="select" label="Host taxon ID type">
                <option value="integer" selected="True">Value</option>
                <option value="tsv">File</option>
            </param>
            <when value="integer">
                <param name="host_taxID_int" type="integer" label="Host taxon ID value" value="83333" help="default: 83333 [E. coli K12]" />
            </when>
            <when value="tsv">
                <param name="host_taxID_file" type="data" format="tsv" label="Host taxon ID file" />
            </when>
        </conditional>
        <section name="adv" title="Advanced Options" expanded="false">
            <param name="enzyme_taxIDs" type="text" value="" label="Comma separated taxon IDs of output enzyme sequences" />
            <param name="nb_ids" type="integer" value="-1" label="Number of uniprot IDs with top score to keep" help=" Number of enzyme IDs to display in results (after taxon IDs filtering) [default = -1 (no limit)]" />
            <param name="nb_targets" type="integer" value="500" min="1" label="Number of targets to display in results" help="Number of targets to display in results (before taxon IDs filtering) [default = 500]" />
            <param name="direction" type="float" value="0" label="Use similarity values for preferred reaction direction only" help="You can choose to rank similarities in both reaction directions or to use only the direction of the reaction based on a consensus list that has been generated according to reaction information based on curated information from MetaCyc (Metabolic Pathway Database) [default=0 (OFF)]" />
            <param argument="--NoMSA" type="boolean" falsevalue="--NoMSA" truevalue="" checked="true" display="checkboxes" label="Do not compute MSA/conservation scores ?" help="Do not compute Multiple Sequence Alignment and conservation scores ? (MSA scores are computed by default)" />