comparison vapor.xml @ 1:7bf891a13ace draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vapor commit 8417888e4ecc1fd033d3412957c5475e29f66403

0:3fe0d1df3950

<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>
        Classify Influenza samples from raw short read sequence data
    </description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.2</token>

            -q
        > out_file
    ]]>    </command>
    <inputs>
        <param name="fasta_file" format="fasta" type="data" label="FASTA file" help="Raw short read sequences (full length reference segment sequences)" />
        <param name="fastq_file" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file(s)" help="WGS reads" />
        <param name="output_type" type="select" label="Output type">
            <option value="scores" selected="true">Return scores only</option>
            <option value="fasta">Return FASTA only</option>
        </param>
        <section name="opt" title="Optional arguments" expanded="true">

            <param name="min_kmer_prop" type="float" value="0.1" label="Min kmer proportion" help="Minimum proportion of matched kmers allowed for queries" />
            <param name="top_seed_frac" type="float" min="0.0" max="1.0" value="0.2" label="Fraction of best seeds to extend" help="" />
        </section>
    </inputs>
    <outputs>
        <data name="output_scores" from_work_dir="out_file" format="tabular" label="VAPOR: closest reference">
            <filter>output_type == "scores"</filter>
            <actions>
                <action name="column_names" type="metadata" default="% of query bases in reads,Total score,Query length,Mean score,Reads after culling,Query description" />
            </actions>
        </data>
        <data name="output_fasta" from_work_dir="out_file" format="fasta" label="VAPOR: closest reference (fasta)">
            <filter>output_type == "fasta"</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" value="test_reads.fq" />
            <output name="output_scores" file="output1.tab" />
        </test>
        <test expect_num_outputs="1">
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" value="test_reads.fq" />

1:7bf891a13ace

<tool id="vapor" name="VAPOR" version="@TOOL_VERSION@+galaxy1" profile="21.05">
    <description>
        Classify Influenza samples from raw short read sequence data
    </description>
    <macros>
        <token name="@TOOL_VERSION@">1.0.2</token>

            -q
        > out_file
    ]]>    </command>
    <inputs>
        <param name="fasta_file" format="fasta" type="data" label="FASTA file" help="Raw short read sequences (full length reference segment sequences)" />
        <param name="fastq_file" format="fastq,fastq.gz,fastqsanger,fastqsanger.gz" type="data" multiple="true" label="FASTQ file(s)" help="WGS reads" />
        <param name="output_type" type="select" label="Output type">
            <option value="scores" selected="true">Return scores only</option>
            <option value="fasta">Return FASTA only</option>
        </param>
        <section name="opt" title="Optional arguments" expanded="true">

            <param name="min_kmer_prop" type="float" value="0.1" label="Min kmer proportion" help="Minimum proportion of matched kmers allowed for queries" />
            <param name="top_seed_frac" type="float" min="0.0" max="1.0" value="0.2" label="Fraction of best seeds to extend" help="" />
        </section>
    </inputs>
    <outputs>
        <data name="output_scores" from_work_dir="out_file" format="tabular" label="${tool.name} on ${on_string}: closest reference scores">
            <filter>output_type == "scores"</filter>
            <actions>
                <action name="column_names" type="metadata" default="% of query bases in reads,Total score,Query length,Mean score,Reads after culling,Query description" />
            </actions>
        </data>
        <data name="output_fasta" from_work_dir="out_file" format="fasta" label="${tool.name} on ${on_string}: closest reference fasta">
            <filter>output_type == "fasta"</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="1">
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" value="test_reads.fq" />
            <output name="output_scores" file="output1.tab" />
        </test>
        <test expect_num_outputs="1">
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" value="test_reads.fastqsanger.gz" />
            <output name="output_scores" file="output1.tab" />
        </test>
        <test expect_num_outputs="1">
            <param name="fasta_file" value="HA_sample.fa" />
            <param name="fastq_file" value="test_reads.fq" />