comparison gene_family_classifier.xml @ 6:e813f9537cb2 draft

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5:fd170580a6c9

        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.0.3">plant_tribes_gene_family_classifier</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
#if str($options_type.options_type_selector) == 'advanced':
    #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
    #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
    #set create_orthogroup_cond = $options_type.create_orthogroup_cond

#end if
    ]]></command>
    <inputs>
        <param name="input" format="fasta" type="data" label="Proteins fasta file"/>
        <expand macro="param_scaffold" />
        <param name="method" type="select" label="Protein clustering method">
            <option value="gfam" selected="true">GFam</option>
            <option value="orthofinder">OrthoFinder</option>
            <option value="orthomcl">OrthoMCL</option>
        </param>
        <conditional name="save_hmmscan_log_cond">
            <param name="classifier" type="select" label="Protein classifier">
                <option value="blastp" selected="true">blastp</option>
                <option value="hmmscan">hmmscan</option>
                <option value="both">Both blastp and hmmscan</option>

6:e813f9537cb2

        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="1.0.3">plant_tribes_gene_family_classifier</requirement>
    </requirements>
    <code file="get_clustering_methods.py"/>
    <command detect_errors="exit_code"><![CDATA[
#if str($options_type.options_type_selector) == 'advanced':
    #set specify_super_orthogroups_cond = $options_type.specify_super_orthogroups_cond
    #set specify_super_orthogroups = $specify_super_orthogroups_cond.specify_super_orthogroups
    #set create_orthogroup_cond = $options_type.create_orthogroup_cond

#end if
    ]]></command>
    <inputs>
        <param name="input" format="fasta" type="data" label="Proteins fasta file"/>
        <expand macro="param_scaffold" />
        <expand macro="param_method" />
        <conditional name="save_hmmscan_log_cond">
            <param name="classifier" type="select" label="Protein classifier">
                <option value="blastp" selected="true">blastp</option>
                <option value="hmmscan">hmmscan</option>
                <option value="both">Both blastp and hmmscan</option>