comparison nextalign.xml @ 8:1c785a6b4d90 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 017e25729a8ffd3722e87dfdf10ff4fd99c0babd"

7:4771f8bc8fa4

    --max-indel '${max_indel}'
    --nuc-seed-length '${nuc_seed_length}'
    --nuc-min-seeds '${nuc_min_seeds}'
    --nuc-seed-spacing '${nuc_seed_spacing}'
    --nuc-mismatches-allowed '${nuc_mismatches_allowed}'
    --aa-seed-length '${aa_seed_length}'
    --aa-min-seeds '${aa_min_seeds}'
    --aa-seed-spacing '${aa_seed_spacing}'
    --aa-mismatches-allowed '${aa_mismatches_allowed}'
    ]]></command>
    <inputs>
        <expand macro="reference"/>
        <param argument="--sequences" type="data" format="fasta" label="FASTA file with input sequences"/>
        <param argument="--output-insertions" type="boolean" checked="true" label="Output insertion sequences?" help="Outputs stripped insertions relative to reference as CSV"/>

        <param argument="--nuc-seed-spacing" type="integer" value="100" min="0"
            label="Spacing between seeds during nucleotide alignment." />
        <param argument="--nuc-mismatches-allowed" type="integer" value="3" min="0"
            label="Maximum number of mismatching nucleotides."
            help="Maximum number of mismatching nucleotides allowed for a seed to be considered a match." />
        <param argument="--aa-seed-length" type="integer" value="12" min="1"
            label="Seed length for aminoacid alignment" />
        <param argument="--aa-min-seeds" type="integer" value="10" min="1"
            label="Minimum number of seeds to search for during aminoacid alignment."
            help="Relevant for short sequences. In long sequences, the number of seeds is determined by the aminoacid seed spacing." />
        <param argument="--aa-seed-spacing" type="integer" value="100" min="0"
            label="Spacing between seeds during aminoacid alignment." />
        <param argument="--aa-mismatches-allowed" type="integer" value="2" min="0"
            label="Maximum number of mismatching aminoacids."
            help="Maximum number of mismatching aminoacids allowed for a seed to be considered a match." />
    </inputs>
    <outputs>
        <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/>
        <data name="output_csv" format="csv" label="${tool.name} on ${on_string} (CSV)">
            <filter>output_insertions</filter>

8:1c785a6b4d90

    --max-indel '${max_indel}'
    --nuc-seed-length '${nuc_seed_length}'
    --nuc-min-seeds '${nuc_min_seeds}'
    --nuc-seed-spacing '${nuc_seed_spacing}'
    --nuc-mismatches-allowed '${nuc_mismatches_allowed}'
    ]]></command>
    <inputs>
        <expand macro="reference"/>
        <param argument="--sequences" type="data" format="fasta" label="FASTA file with input sequences"/>
        <param argument="--output-insertions" type="boolean" checked="true" label="Output insertion sequences?" help="Outputs stripped insertions relative to reference as CSV"/>

        <param argument="--nuc-seed-spacing" type="integer" value="100" min="0"
            label="Spacing between seeds during nucleotide alignment." />
        <param argument="--nuc-mismatches-allowed" type="integer" value="3" min="0"
            label="Maximum number of mismatching nucleotides."
            help="Maximum number of mismatching nucleotides allowed for a seed to be considered a match." />
    </inputs>
    <outputs>
        <data name="output_fasta" format="fasta" label="${tool.name} on ${on_string} (FASTA)"/>
        <data name="output_csv" format="csv" label="${tool.name} on ${on_string} (CSV)">
            <filter>output_insertions</filter>