annotate macros.xml @ 1:a671907f96fe draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tools/coverm commit 2388df7187533fb66b7729730340d2eb7b93c112

<macros>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">coverm</requirement>
        </requirements>
    </xml>
    <token name="@INPUT_FORMATS@">fasta,fastq,fastq.gz,fasta.gz</token>
    <token name="@TOOL_VERSION@">0.6.1</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="citation">
        <citations>
            <citation type="bibtex">
            @misc{githubCoverm,
            author = {B J. Woodcroft},
            year = {2021},
            title = {CoverM},
            publisher = {GitHub},
            journal = {GitHub repository},
            url = {https://github.com/wwood/CoverM}
            }
            </citation>
        </citations>
    </xml>
    <xml name="genome_opt">
        <conditional name="genome">
            <param name="ref_or_genome" type="select" label="Select if you want to specify additional genome files.">
                <option value="genomic">yes</option>
                <option value="none" selected="true">No (Only when BAM files are provided)</option>
            </param>
            <when value="none">
                <param argument="--single-genome" type="boolean" truevalue="--single-genome" falsevalue="" checked="false" label="All contigs are from the same genome."/>
                <param type="text" name="separator" optional="true" label="Character, that separates genome names from contig names in the reference file." >
                    <sanitizer>
                        <valid initial="string.punctuation">
                        </valid>
                    </sanitizer>
                </param>
            </when>
            <when value="genomic">
                <conditional name="genomic">
                    <param type="select" label="Reference genome source" name="source">
                        <option value="history" selected="true">History</option>
                        <option value="builtin">Built-in</option>
                    </param>
                    <when value="history">
                        <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" />
                    </when>
                    <when value="builtin">
                        <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)">
                            <options from_data_table="all_fasta" />
                        </param>
                    </when>
                </conditional>
            </when>
        </conditional>
    </xml>
    <xml name="genome">
        <conditional name="genome">
            <param name="ref_or_genome" type="select" label="Reference sequence mode" help="Select if you want to specify genome file(s) or a FASTA reference file or both. NOTE: If genomic FASTA files are specified, then reference is not needed as a reference FASTA file can be derived by concatenating input genomes. However, while not necessary, reference can be specified if an alternate reference sequence set is desired.">
                <option value="genomic" selected="true">Reference genome</option>
                <option value="reference">Contigs (e.g. concatenated genomes or metagenome assembly)</option>
            </param>
            <when value="genomic">
                <conditional name="genomic">
                    <param type="select" label="Reference genome source" name="source">
                        <option value="history" selected="true">History</option>
                        <option value="builtin">Built-in</option>
                    </param>
                    <when value="history">
                        <param type="data" name="fasta_history" multiple="true" label="FASTA files of each genome" format="fasta" />
                    </when>
                    <when value="builtin">
                        <param type="select" name="fasta_builtin" multiple="true" label="Reference genome(s)">
                            <options from_data_table="all_fasta" />
                        </param>
                    </when>
                </conditional>
            </when>
            <when value="reference">
                <param type="data" name="ref_source" multiple="true" label="Contigs file(s)" format="fasta" help="If multiple references FASTA files are provided and 'sharded' is specified, then reads will be mapped to references separately as sharded BAMs."/>
                <conditional name="cond_single_genome">
                    <param name="single_genome" type="select" label="All contigs are from a single genome">
                        <option value="--single-genome">True</option>
                        <option value="false">False</option>
                    </param>
                    <when value="--single-genome">
                        <param type="data" name="genome_definition" format="tsv" optional="true" label="File containing newline-separated list of genome_name and contig, separated by tab, to define the genome of each contig." />
                    </when>
                    <when value="false">
                        <param type="text" argument="--separator" optional="true" label="Character, that separates genome names from contig names in the reference file." >
                            <sanitizer>
                                <valid initial="string.punctuation">
                                </valid>
                            </sanitizer>
                        </param>
                    </when>
                </conditional>                    
                <conditional name="add_genome">
                    <param name="add_genome" type="select" label="Add additional Genome Files">
                        <option value="true">Yes</option>
                        <option value="false" selected="true">No</option>
                    </param>
                    <when value="true">
                        <conditional name="add_genomic">
                            <param type="select" label="Reference genome source" name="source">
                                <option value="history" selected="true">History</option>
                                <option value="builtin">Built-in</option>
                            </param>
                            <when value="history">
                                <param type="data" name="fasta_history" multiple="true" label="Single FASTA file of contigs" format="fasta" />
                            </when>
                            <when value="builtin">
                                <param type="select" name="fasta_builtin" multiple="true" label="Reference genome">
                                    <options from_data_table="all_fasta" />
                                </param>
                            </when>
                        </conditional>                           
                    </when>
                    <when value="false">
                    </when>
                </conditional>
            </when>
        </conditional>
    </xml>
    <xml name="reads_for_contig">
        <conditional name="reads">
            <param type="select" label="Read type" name="read_type">
                <option value="paired">Paired end</option>
                <option value="paired_collection" selected="true">Paired collection</option>
                <option value="single">Single ended</option>
                <option value="interleaved">Interleaved</option>
                <option value="bam">BAM file(s)</option>
            </param>
            <when value="paired">
                <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" />
                <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" />
                <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
            </when>
            <when value="paired_collection">
                <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order" />
                <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
            </when>
            <when value="single">
                <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" />
                <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
            </when>
            <when value="interleaved">
                <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" />
                <param type="data" name="ref_fasta_history" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
            </when>
            <when value="bam">
                 <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" help="BAM file(s). These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n). When specified, no read mapping algorithm is undertaken."/>
                <param type="data" name="ref_fasta_history" optional="true" multiple="true" label="FASTA file(s) of contigs" format="fasta" />
            </when>
        </conditional>
    </xml>     
    <xml name="reads">
        <conditional name="reads">
            <param type="select" label="Read type" name="read_type">
                <option value="single">Single ended</option>
                <option value="paired">Paired end</option>
                <option value="paired_collection" selected="true">Paired collection</option>
                <option value="interleaved">Interleaved</option>
                <option value="bam">BAM file(s)</option>
            </param>
            <when value="paired">
                <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" />
                <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" />
                <expand macro="genome"/>
            </when>
            <when value="paired_collection">
                <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="Collection of paired-reads" help="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order." />
                <expand macro="genome"/>
            </when>
            <when value="single">
                <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Single Read" />
                <expand macro="genome"/>
            </when>
            <when value="interleaved">
                <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" />
                <expand macro="genome"/>
            </when>
            <when value="bam">
                <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" help="BAM file(s). These must be reference sorted (e.g. with samtools sort) unless sharded is specified, in which case they must be read name sorted (e.g. with samtools sort -n). When specified, no read mapping algorithm is undertaken."/>
                <expand macro="genome_opt"/>
            </when>
        </conditional>
    </xml>
    <xml name="add_reads">
        <section name="add_reads" title="Add an additional read">
            <conditional name="extra_read">
                <param type="select" label="Read type" name="read_type">
                    <option value="none" selected="true">None</option>
                    <option value="paired">Paired end</option>
                    <option value="paired_collection">Paired collection</option>
                    <option value="single">Single ended</option>
                    <option value="interleaved">Interleaved</option>
                    <option value="bam">BAM file(s)</option>
                </param>
                <when value="none">
                </when>
                <when value="paired">
                    <param type="data" format="@INPUT_FORMATS@" name="read1" multiple="true" label="Read1" />
                    <param type="data" format="@INPUT_FORMATS@" name="read2" multiple="true" label="Read2" />
                </when>
                <when value="paired_collection">
                    <param type="data_collection" collection_type="list:paired" format="@INPUT_FORMATS@" name="paired_reads" label="One or more pairs of forward and reverse possibly gzipped FASTA/Q files for mapping in order" />
                </when>
                <when value="single">
                    <param type="data" format="@INPUT_FORMATS@" name="single" multiple="true" label="Single read" />
                </when>
                <when value="interleaved">
                    <param type="data" format="@INPUT_FORMATS@" multiple="true" name="single" label="Interleaved" />
                </when>
                <when value="bam">
                    <param type="data" format="bam" name="bam" multiple="true" label="BAM file(s)" />
                </when>
            </conditional>
        </section>
    </xml>
    <xml name="mapping">
        <section name="mapping" title="Mapping options" expanded="false">
            <param argument="--mapper" optional="true" type="select" label="Mapper" help="Underlying mapping software used. Default: minimap2-sr" >
                <option value="minimap2-sr">minimap2 with '-x sr' option</option>
                <option value="minimap2-ont">minimap2 with '-x map-ont' option</option>
                <option value="minimap2-pb">minimap2 with '-x map-pb' option</option>
                <option value="minimap2-no-preset">minimap2 with no '-x' option</option>
                <option value="bwa-mem">BWA-MEM using default parameters</option>
            </param>
            <param argument="--min_read-aligned-length" type="integer" min="0" value="0" 
                label="Min read aligned length" help="Exclude reads with smaller numbers of aligned bases. Default: 0" />
            <param argument="--min_read-percent-identity" type="float" min="0" max="100" value="0" 
                label="Min read percent identity" help="Exclude reads by overall percent identity e.g. 95 for 95%. Default: 0" />
            <param argument="--min_read-aligned-percent" type="float" min="0" max="100" value="0" 
                label="Min read aligned percentage" help="Exclude reads by percent aligned bases e.g. 95 means 95% 
                    of the read's bases must be aligned. Default: 0" />
            <param argument="--min_read-aligned-length-pair" type="integer" min="0" value="0" 
                label="Min read aligned length pair" help="Exclude pairs with smaller numbers of aligned bases. 
                    Implies --proper-pairs-only. Default: 0" />
            <param argument="--min_read-percent-identity-pair" type="float" min="0" max="100" value="0" 
                label="Min read percent identity pair" help="Exclude pairs by overall percent identity e.g. 95 for 95%. 
                    Implies --proper-pairs-only. Default: 0" />
            <param argument="--min_read-aligned-percent-pair" type="float" min="0" max="100" value="0" 
                label="Min read aligned percentage pair" help="Exclude reads by percent aligned bases e.g. 95 means 95% of 
                    the read's bases must be aligned. Implies --proper-pairs-only. Default: 0" />
            <param argument="--proper-pairs-only" type="boolean" truevalue="--proper-pairs-only" falsevalue="" 
                label="Require reads to be mapped as proper pairs" help="Default: not set"/>
            <param argument="--exclude-supplementary" type="boolean" truevalue="--exclude-supplementary" falsevalue="" 
                label="Exclude supplementary alignments" help="Default: not set"/>
        </section>
    </xml>
    <xml name="coverage">
        <section name="cov" title="Coverage calculation options" expanded="false">
            <param name="relative_abundance" type="boolean" falsevalue="" truevalue="relative_abundance" label="Relative abundance (default)"/>
            <param name="mean" type="boolean" falsevalue="" truevalue="mean" label="Mean"/>
            <conditional name="cond_methods">
                <param name="trimmed_mean" type="select" label="Trimmed mean">
                    <option value="trimmed_mean">Yes</option>
                    <option value="" selected="true">No</option>
                </param>
                <when value="trimmed_mean">
                    <param name="trim_min" type="integer" min="0" value="5" label="Trim min" help="Remove this smallest fraction of positions when calculating trimmed_mean default: 5"/>
                    <param name="trim_max" type="integer" min="0" value="95" label="Trim max" help="Maximum fraction for trimmed_mean calculations default: 95"/>
                </when>
                <when value=""/>
            </conditional>
            <param name="covered_bases" type="boolean" falsevalue="" truevalue="covered_bases" label="Covered bases"/>
            <param name="covered_fraction" type="boolean" falsevalue="" truevalue="covered_fraction" label="Covered fraction"/>
            <param name="variance" type="boolean" falsevalue="" truevalue="variance" label="Variance"/>
            <param name="length" type="boolean" falsevalue="" truevalue="length" label="Length"/>
            <param name="count" type="boolean" falsevalue="" truevalue="count" label="Count"/>
            <param name="metabat" type="boolean" falsevalue="" truevalue="metabat" label="MetaBAT"/>
            <param name="coverage_histogram" type="boolean" falsevalue="" truevalue="coverage_histogram" label="Coverage histogram"/>
            <param name="reads_per_base" type="boolean" falsevalue="" truevalue="reads_per_base" label="Reads per base"/>
            <param name="rpkm" type="boolean" falsevalue="" truevalue="rpkm" label="RPKM"/>
            <param name="tpm" type="boolean" falsevalue="" truevalue="tpm" label="TPKM"/>
            <param name="min_covered_fraction" type="integer" min="0" optional="true"
                label="Min covered fraction" help="Genomes with less coverage than this reported as having zero coverage. Default: 10"/>
            <param name="contig_end_exclusion" type="integer" min="0" optional="true"
                label="Contig end exclusion" help="Exclude bases at the ends of reference sequences from calculation. Default: 75"/>
        </section>
    </xml>
    <xml name="out">
        <section name="out" title="Output options" expanded="false">
            <param name="output_format" type="select" label="Shape of output" help="'Sparse' for long format, 'dense' for species-by-site. Default: dense]">
                <option value="dense" selected="true">Dense</option>
                <option value="sparse">Sparse</option>
            </param>
            <param name="no_zeros" type="boolean" truevalue="--no-zeros" falsevalue="" optional="true" label="Omit printing of genomes that have zero coverage" />
            <param argument="--dereplication-output-cluster-definition" type="boolean" truevalue="--dereplication-output-cluster-definition" falsevalue="" label="Output a file of representative TAB member lines." />
            <param argument="--dereplication-output-representative-fasta-directory-copy" type="boolean" truevalue="--dereplication-output-representative-fasta-directory-copy" falsevalue="" label="Output representative genomes" />
        </section>
    </xml>
    <xml name="citations">
        <citations>
            <yield />
        </citations>
    </xml>
</macros>