comparison dorado.xml @ 7:34e128a6a6ed draft default tip

planemo upload for repository https://github.com/usegalaxy-au/tools-au/tree/master/tools/dorado commit 97793e41864a750b1c18c80b858c118e43ae8d97

6:5e67ea368004

<tool id="dorado" name="Dorado" version="@VERSION@+galaxy0" python_template_version="3.5" profile="24.1">
    <description>basecaller for raw Oxford Nanopore data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>

> summary.tsv

    ]]></command>
    <inputs>
        <param name="pod5_file" type="data" format="pod5" label="Raw pod5 file" help="Only pod5 is supported. You can convert fast5 to pod5 with the fast5 to pod5 tool."/>
        <param name="model" type="select" label="Basecalling model. See the Help section for info on model names.">
            <options from_data_table="dorado_models">
                <!-- only allow models that shipped in this container -->
                <filter type="static_value" column="1" value="@CONTAINER_HASH@"/>
            </options>
        </param>
        <param type="select" argument="--trim" label="DNA adapter and primer trimming" help="Detect and remove any adapter and/or primer sequences from the beginning and end of DNA reads. Note that if you intend to demultiplex the reads, trimming adapters and primers could interfere with correct demultiplexing.">
            <option value="all" selected="true">Any. Trim any detected adapters or primers.</option>
            <option value="primers"> Primers. Trim any detected adapters or primers, but if barcoding is enabled the barcode sequences will not be trimmed.</option>
            <option value="adapters"> Adapters. Trim any detected adapters, but primers will not be trimmed, and if barcoding is enabled then barcodes will not be trimmed either.</option>
            <option value="none"> None. Nothing will be trimmed.</option>
        </param>
        <!-- dev note: the barcode kits are hardcoded in https://github.com/nanoporetech/dorado/blob/release-v0.9/dorado/utils/barcode_kits.cpp -->
        <param type="select" argument="--kit-name" optional="true" label="Enable barcoding with the selected kit name." help="Reads are classified into their barcode groups during basecalling. The classification will be reflected in the read group name as well as in the BC tag of the output record.">
            <expand macro="barcode_kits" />
        </param>
    </inputs>
    <outputs>
        <data format="unsorted.bam" name="out_bam" label="Reads from ${on_string} basecalled by ${tool.name} with model ${model.fields.name}" from_work_dir="calls.bam"/>
        <data format="tsv" name="out_tsv" label="${tool.name} sequencing summary for ${on_string}" from_work_dir="summary.tsv"/>

7:34e128a6a6ed

<tool id="dorado" name="Dorado" version="@VERSION@+galaxy1" python_template_version="3.5" profile="24.1">
    <description>basecaller for raw Oxford Nanopore data</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>

> summary.tsv

    ]]></command>
    <inputs>
        <param name="pod5_file" type="data" format="pod5" label="Raw pod5 file" help="Only pod5 is supported. You can convert fast5 to pod5 with the fast5 to pod5 tool."/>
        <expand macro="model_param"/>
        <param type="select" argument="--trim" label="DNA adapter and primer trimming" help="Detect and remove any adapter and/or primer sequences from the beginning and end of DNA reads. Note that if you intend to demultiplex the reads, trimming adapters and primers could interfere with correct demultiplexing.">
            <option value="all" selected="true">Any. Trim any detected adapters or primers.</option>
            <option value="primers"> Primers. Trim any detected adapters or primers, but if barcoding is enabled the barcode sequences will not be trimmed.</option>
            <option value="adapters"> Adapters. Trim any detected adapters, but primers will not be trimmed, and if barcoding is enabled then barcodes will not be trimmed either.</option>
            <option value="none"> None. Nothing will be trimmed.</option>
        </param>
        <!-- dev note: the barcode kits are hardcoded in https://github.com/nanoporetech/dorado/blob/release-v0.9/dorado/utils/barcode_kits.cpp -->
        <param type="select" argument="--kit-name" optional="true" label="Enable barcoding with the selected kit name." help="Reads are classified into their barcode groups during basecalling. The classification will be reflected in the read group name as well as in the BC tag of the output record.">
            <expand macro="barcode_kits"/>
        </param>
    </inputs>
    <outputs>
        <data format="unsorted.bam" name="out_bam" label="Reads from ${on_string} basecalled by ${tool.name} with model ${model.fields.name}" from_work_dir="calls.bam"/>
        <data format="tsv" name="out_tsv" label="${tool.name} sequencing summary for ${on_string}" from_work_dir="summary.tsv"/>