comparison virhunter.xml @ 3:302332b914ef draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/VirHunter commit 58587e05f604590c70550e13fc51b7425e916ed4

2:ea2cccb9f73e

        --test_ds '${fasta_file}'
        --weights '${weights.fields.path}'
        --out_path '${predicted_fragments.extra_files_path}'
        --return_viral True
        --limit $limit
    && cp '${predicted_fragments.extra_files_path}'/predicted_fragments.csv predicted_fragments.csv
    && cp '${predicted_fragments.extra_files_path}'/predicted.csv predicted.csv
    && cp '${predicted_fragments.extra_files_path}'/viral.fasta viral.fasta

    ]]></command>
    <inputs>
        <param name="fasta_file" type="data" format="fasta" label="DNA FASTA file"/>

            </options>
        </param>
        <param argument="--limit" type="integer" min="0" value="750" label="Minimum contig length" help="Do not predict contigs shorter than this value. Default: 750" />
    </inputs>
    <outputs>
        <data format="csv" name="predicted_fragments" from_work_dir="predicted_fragments.csv" label="${tool.name} on ${on_string}: predicted fragments"/>
        <data format="csv" name="predicted" from_work_dir="predicted.csv" label="${tool.name} on ${on_string}: predicted "/>
        <data format="fasta" name="viral" from_work_dir="viral.fasta" label="${tool.name} on ${on_string}: viral FASTA file" />
    </outputs>
    <tests>
        <test>
            <param name="fasta_file" value="viruses.fasta"/>
            <param name="weights" value="test"/>
            <output name="predicted_fragments" file="predicted_fragments.csv"  ftype="csv" lines_diff="2"/>
            <output name="predicted" file="predicted.csv"  ftype="csv" lines_diff="2"/>
            <output name="viral" file="viral.fasta"  ftype="fasta" lines_diff="2"/>
        </test>
    </tests>

    <help>

3:302332b914ef

        --test_ds '${fasta_file}'
        --weights '${weights.fields.path}'
        --out_path '${predicted_fragments.extra_files_path}'
        --return_viral True
        --limit $limit
    && cp '${predicted_fragments.extra_files_path}'/predicted_fragments.tsv predicted_fragments.tsv
    && cp '${predicted_fragments.extra_files_path}'/predicted.tsv predicted.tsv
    && cp '${predicted_fragments.extra_files_path}'/viral.fasta viral.fasta

    ]]></command>
    <inputs>
        <param name="fasta_file" type="data" format="fasta" label="DNA FASTA file"/>

            </options>
        </param>
        <param argument="--limit" type="integer" min="0" value="750" label="Minimum contig length" help="Do not predict contigs shorter than this value. Default: 750" />
    </inputs>
    <outputs>
        <data format="tabular" name="predicted_fragments" from_work_dir="predicted_fragments.tsv" label="${tool.name} on ${on_string}: predicted fragments"/>
        <data format="tabular" name="predicted" from_work_dir="predicted.tsv" label="${tool.name} on ${on_string}: predicted "/>
        <data format="fasta" name="viral" from_work_dir="viral.fasta" label="${tool.name} on ${on_string}: viral FASTA file" />
    </outputs>
    <tests>
        <test>
            <param name="fasta_file" value="viruses.fasta"/>
            <param name="weights" value="test"/>
            <output name="predicted_fragments" file="predicted_fragments.tsv"  ftype="tabular" lines_diff="2"/>
            <output name="predicted" file="predicted.tsv"  ftype="tabular" lines_diff="2"/>
            <output name="viral" file="viral.fasta"  ftype="fasta" lines_diff="2"/>
        </test>
    </tests>

    <help>