<macros>
    <token name="@TOOL_VERSION@">39.01</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <token name="@PROFILE@">22.01</token>
    <xml name="edam_ontology">
        <edam_topics>
            <edam_topic>topic_0622</edam_topic> <!-- Genomics -->
            <edam_topic>topic_0091</edam_topic> <!-- Bioinformatics -->
        </edam_topics>
        <edam_operations>
            <edam_operation>operation_0496</edam_operation> <!-- Global alignment -->
            <edam_operation>operation_0491</edam_operation> <!-- Pairwise sequence alignment -->
        </edam_operations>
    </xml>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">bbmap</requirement>
            <requirement type="package" version="1.16.1">samtools</requirement> <!-- automatic solving installs 1.6 in some cases, instead -->
        </requirements>
    </xml>
    <macro name="dbKeyActionsBBMap">
        <expand macro="dbKeyActions">
            <option type="from_data_table" name="fasta_indexes" column="1" offset="0">
                <filter type="param_value" column="0" value="#" compare="startswith" keep="False"/>
                <filter type="param_value" ref="ref_source_cond.reference" column="1"/>
            </option>
        </expand>
    </macro>
    <macro name="dbKeyActions">
        <actions>
            <conditional name="ref_source_cond.ref_source">
                <when value="cached">
                    <action type="metadata" name="dbkey">
                        <yield/>
                    </action>
                </when>
                <when value="history">
                    <action type="metadata" name="dbkey">
                        <option type="from_param" name="ref_source_cond.reference" param_attribute="dbkey"/>
                    </action>
                </when>
            </conditional>
        </actions>
    </macro>
    <macro name="input_type_cond">
        <conditional name="input_type_cond">
            <param name="input_type" type="select" label="Choose the category of the files to be analyzed">
                <option value="single" selected="true">Single dataset</option>
                <option value="pair">Dataset pair</option>
                <option value="paired">List of dataset pairs</option>
            </param>
            <when value="single">
                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Fastq file"/>
            </when>
            <when value="pair">
                <param name="read1" type="data" format="fastqsanger.gz,fastqsanger" label="Forward reads fastq file"/>
                <param name="read2" type="data" format="fastqsanger.gz,fastqsanger" label="Reverse reads fastq file"/>
            </when>
            <when value="paired">
                <param name="reads_collection" type="data_collection" format="fastqsanger,fastqsanger.gz" collection_type="paired" label="Collection of fastqsanger paired read files"/>
            </when>
        </conditional>
    </macro>
    <macro name="reference_source_cond">
        <conditional name="ref_source_cond">
            <param name="ref_source" type="select" label="Select reference genome source; a cached reference or one from the history">
                <option value="cached" selected="True">Use a cached reference</option>
                <option value="history">Use a reference from the history</option>
            </param>
            <when value="cached">
                <param name="reference" type="select" label="Using reference genome">
                    <options from_data_table="fasta_indexes">
                        <filter type="sort_by" column="2"/>
                        <validator type="no_options" message="A built-in reference genome is not available"/>
                    </options>
                </param>
            </when>
            <when value="history">
                <param name="reference" type="data" format="fasta" label="Using reference genome"/>
            </when>
        </conditional>
    </macro>
    <macro name="ktrim_cond">
        <conditional name="ktrim_cond">
            <param name="ktrim_select"  type="select" label="Trim reads to remove bases matching reference kmers?">
                <option value="no" selected="true">No</option>
                <option value="yes">Yes</option>
            </param>
            <when value="no"/>
            <when value="yes">
                <param argument="ktrim"  type="select" label="Select trimming position">
                    <option value="r">Trim to the right</option>
                    <option value="l">Trim to the left</option>
                </param>
                <param argument="minlength" type="integer" value="10" label="Minimum read length" help="Trimmed reads shorter than this will be discarded, pairs will be discarded if both are shorter."/>
             </when>
        </conditional>
    </macro>
    <xml name="citations">
        <citations>
            <citation type="doi">
                https://doi.org/10.1371/journal.pone.0185056
            </citation>
        </citations>
    </xml>
</macros>