comparison gene_family_aligner.xml @ 7:2ac7090847f9 draft

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6:3384b6a842b0

        #if str($remove_sequences_with_gaps_cond.iterative_realignment):
            --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
        #end if
    #end if
#end if
&>proc.log
    ]]></command>
    <inputs>
        <param name="input" format="fasta" type="data_collection" collection_type="list" label="Integrated orthogroup fasta files" />
        <conditional name="alignment_method_cond">
            <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">

        </collection>
        <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}">
            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
            <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
        </collection>

    </outputs>
    <tests>
        <test>
            <param name="input">
                <collection type="list">

7:2ac7090847f9

        #if str($remove_sequences_with_gaps_cond.iterative_realignment):
            --iterative_realignment $remove_sequences_with_gaps_cond.iterative_realignment
        #end if
    #end if
#end if
&>gene_family_aligner_log.txt;
if [[ $? -ne 0 ]]; then
    find geneFamilyAlignments_dir -type d -maxdepth 1 -exec cp gene_family_aligner_log.txt {} \;
    exit 1;
fi
    ]]></command>
    <inputs>
        <param name="input" format="fasta" type="data_collection" collection_type="list" label="Integrated orthogroup fasta files" />
        <conditional name="alignment_method_cond">
            <param name="alignment_method" type="select" force_select="true" label="Multiple sequence alignment method">

        </collection>
        <collection name="filtered_fna" type="list" label="${tool.name} (filtered orthogroup codon alignments) on ${on_string}">
            <discover_datasets pattern="__name__" directory="geneFamilyAlignments_dir/orthogroups_filtered_aln_fna" format="fasta" />
            <filter>codon_alignments == 'yes' and remove_gappy_sequences_cond['remove_gappy_sequences'] == 'yes' and remove_gappy_sequences_cond['remove_sequences_with_gaps_cond']['remove_sequences_with_gaps'] == 'yes'</filter>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="input">
                <collection type="list">