annotate hisat2_macros.xml @ 25:3fb01a8c902d draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hisat2 commit b7df8879a0f5d75c8562700fe9b5dc9e8173a652

<macros>
    <xml name="paired_end_options">

        <param name="rna_strandness" argument="--rna-strandness" type="select" label="Specify strand information"
                help="'FR' means a read corresponds to a transcript. 'RF' means a read corresponds to the reverse complemented counterpart of a transcript. With this option being used, every read alignment will have an XS attribute tag: '+' means a read belongs to a transcript on '+' strand of genome. '-' means a read belongs to a transcript on '-' strand of genome.">
                <option value="">Unstranded</option>
                <option value="FR">Forward (FR)</option>
                <option value="RF">Reverse (RF)</option>
        </param>

        <conditional name="paired_options">
            <param name="paired_options_selector" type="select" label="Paired-end options" help="See &quot;Alignment Options&quot; section of Help below for information">
                <option value="defaults">Use default values</option>
                <option value="advanced">Specify paired-end parameters</option>
            </param>
            <when value="defaults"/>
            <when value="advanced">
                <param name="fr_rf_ff" argument="--fr/--rf/--ff" type="select" display="radio" label="Select the upstream/downstream mate orientations for a valid paired-end alignment against the forward reference strand"
                       help="E.g., if `--fr` is specified and there is a candidate paired-end alignment where mate 1 appears upstream of the reverse complement of mate 2 and the fragment length constraints (`-I` and `-X`) are met, that alignment is valid.  Also, if mate 2 appears upstream of the reverse complement of mate 1 and all other constraints are met, that too is valid. `--rf` likewise requires that an upstream mate1 be reverse-complemented and a downstream mate2 be forward-oriented. `--ff` requires both an upstream mate 1 and a downstream mate 2 to be forward-oriented; Default=--fr (appropriate for Illumina's Paired-end Sequencing Assay)">
                    <option value="--fr" selected="True">--fr</option>
                    <option value="--rf">--rf</option>
                    <option value="--ff">--ff</option>
                </param>
                <param argument="--no-mixed" name="no_mixed" type="boolean" truevalue="--no-mixed" falsevalue="" checked="False" label="Disable no-mixed behavior" help="By default, when `hisat2` cannot find a concordant or discordant alignment for a pair, it then tries to find alignments for the individual mates; default: False"/>
                <param argument="--no-discordant" name="no_discordant" type="boolean" truevalue="--no-discordant" falsevalue="" checked="False" label="Disable no-discordant behavior" help="--no-discordant; By default, `hisat2` looks for discordant alignments if it cannot find any concordant alignments. A discordant alignment is an alignment where both mates align uniquely, but that does not satisfy the paired-end constraints (`--fr`/`--rf`/`--ff`, `-I`, `-X`); default: False"/>
            </when>
        </conditional>

    </xml>

    <xml name="dbKeyActions">
        <actions>
            <conditional name="reference_genome.source">
                <when value="indexed">
                    <action type="metadata" name="dbkey">
                         <option type="from_data_table" name="hisat2_indexes" column="1">
                            <filter type="param_value" ref="reference_genome.index" column="0"/>
                        </option>
                    </action>
                </when>
                <when value="history">
                    <action type="metadata" name="dbkey">
                        <option type="from_param" name="reference_genome.history_item" param_attribute="dbkey" />
                    </action>
                </when>
            </conditional>
        </actions>
    </xml>

</macros>