macros.xml

<macros>
    <token name="@TOOL_VERSION@">2.2.0</token>
    <token name="@VERSION_SUFFIX@">0</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">diamond</requirement>
        </requirements>
    </xml>
    <xml name="stdio">
        <stdio>
            <regex match="Failed to allocate" source="stderr" level="fatal_oom"/>
        </stdio>
    </xml>
    <xml name="version_command">
        <version_command>diamond version | cut -d" " -f 3</version_command>
    </xml>

    <xml name="output_column_select">
        <param argument="--fields" type="select" label="Tabular fields" help="" multiple="true">
            <option value="qseqid" selected="true">Query Seq - id</option>
            <option value="qlen">Query sequence length</option>
            <option value="sseqid" selected="true">Subject Seq - id</option>
            <option value="sallseqid">All subject Seq - id(s)</option>
            <option value="slen">Subject sequence length</option>
            <option value="qstart" selected="true">Start of alignment in query</option>
            <option value="qend" selected="true">End of alignment in query</option>
            <option value="sstart" selected="true">Start of alignment in subject</option>
            <option value="send" selected="true">End of alignment in subject</option>
            <option value="qseq">Aligned part of query sequence</option>
            <option value="sseq">Aligned part of subject sequence</option>
            <option value="evalue" selected="true">Expect value</option>
            <option value="bitscore" selected="true">Bit score</option>
            <option value="score">Raw score</option>
            <option value="length" selected="true">Alignment length</option>
            <option value="pident" selected="true">Percentage of identical matches</option>
            <option value="nident">Number of identical matches</option>
            <option value="mismatch" selected="true">Number of mismatches</option>
            <option value="positive">Number of positive - scoring matches</option>
            <option value="gapopen" selected="true">Number of gap openings</option>
            <option value="gaps">Total number of gaps</option>
            <option value="ppos">Percentage of positive - scoring matches</option>
            <option value="qframe">Query frame</option>
            <option value="btop">Blast traceback operations(BTOP)</option>
            <option value="stitle">Subject Title</option>
            <option value="salltitles">All Subject Title(s)</option>
            <option value="qcovhsp">Query Coverage Per HSP</option>
            <option value="qtitle">Query title</option>
            <option value="full_sseq">Subject sequence</option>
            <option value="qqual">Query quality values for the aligned part of the query</option>
            <option value="qnum">Query ordinal id</option>
            <option value="snum">Subject ordinal id</option>
            <option value="scovhsp">Subject coverage per HSP</option>
            <option value="full_qqual">Query quality values</option>
            <option value="full_qseq">Query sequence</option>
            <option value="qseq_gapped">Aligned part of query sequence (with gaps)</option>
            <option value="sseq_gapped">Aligned part of subject sequence (with gaps)</option>
            <option value="qstrand">Query strand</option>
            <option value="cigar">Cigar</option>
            <option value="full_qseq_mate">Query sequence of the mate</option>
            <option value="qseq_translated">Translation of the aligned part of query sequence</option>
            <option value="hspnum">Number of HSP within the subject</option>
            <option value="normalized_bitscore">Bitscore normalized by maximum self alignment score</option>
            <option value="normalized_nident">Number of identical matches normalized by maximum length</option>
            <option value="approx_pident">Approximate percentage of identical matches</option>
            <option value="corrected_bitscore" selected="true">Bit score corrected for edge effects</option>
            <yield/>
        </param>
    </xml>

    <xml name="output_type_macro">
        <conditional name="output">
            <param argument="--outfmt" type="select" label="Format of output file" help="">
                <option value="0">BLAST pairwise</option>
                <option value="5">BLAST XML</option>
                <option value="6">BLAST tabular</option>
                <option value="100">DAA</option>
                <option value="101">SAM</option>
                <option value="102">Taxonomic classification</option>
                <option value="104">JSON (flat)</option>
            </param>
            <when value="0"/>
            <when value="5"/>
            <when value="6">
                <expand macro="output_column_select">
                    <yield/>
                </expand>
                <param argument="--header" type="select" label="Use header lines">
                    <option value="0">No</option>
                    <option value="simple">Simple</option>
                    <option value="verbose">Verbose</option>
                </param>
            </when>
            <when value="100">
            </when>
            <when value="101">
            </when>
            <when value="102">
                <param argument="--include-lineage" type="boolean" truevalue="--include-lineage" falsevalue="" checked="false" label="Include lineage in the taxonomic classification format"/>
            </when>
            <when value="104">
                <expand macro="output_column_select">
                    <yield/>
                </expand>
            </when>
        </conditional>
    </xml>
    <xml name="hit_filter_macro">
        <conditional name="filter_score">
            <param name="filter_score_select" type="select" label="Method to filter?" help="(--evalue/--min-score)">
                <option value="evalue" selected="True">Maximum e-value to report alignments</option>
                <option value="min-score">Minimum bit score to report alignments</option>
            </param>
            <when value="evalue">
                <param argument="--evalue" type="float" value="0.001" label="Maximum expected value to keep an alignment"/>
            </when>
            <when value="min-score">
                <param argument="--min-score" type="integer" value="0" label="Minimum bit score to keep an alignment" help="(--min-score)"/>
            </when>
        </conditional>

        <conditional name="hit_filter">
            <param name="hit_filter_select" type="select" label="Method to restrict the number of hits?">
                <option value="max">Maximum number of target sequences</option>
                <option value="top">Percentage of top alignment score</option>
            </param>
            <when value="max">
                <param argument="--max-target-seqs" type="integer" value="25" label="The maximum number of target sequences per query to report alignments for" help="Setting this to 0 will report all alignments that were found."/>
            </when>
            <when value="top">
                <param argument="--top" type="integer" value="0" min="0" max="100" label="Keep alignments within the given percentage range of the top alignment score for a query" help="For example, setting this to 10 will report all alignments whose score is at most 10% lower than the best alignment score for a query."/>
            </when>
        </conditional>
        <param argument="--id" type="float" value="0" min="0" max="100" label="Minimum identity percentage to report an alignment" help="Report only alignments above the given percentage of sequence identity"/>
        <param argument="--approx-id" type="float" value="0" min="0" max="100" label="Minimum approx. identity% to report an alignment"/>
        <param argument="--query-cover" type="float" value="0" min="0" max="100" label="Minimum query cover percentage to report an alignment" help="Report only alignments above the given percentage of query cover"/>
        <param argument="--subject-cover" type="float" value="0" min="0" max="100" label="Minimum subject cover percentage to report an alignment" help="Report only alignments above the given percentage of subject cover"/>
    </xml>
    <xml name="block_size" tokens="value">
        <param argument="--block-size" type="float" value="@VALUE@" min="0" label="Block size in billions of sequence letters to be processed at a time"
            help="This is the main parameter for controlling the program’s memory and disk space usage. Bigger numbers will increase the use of memory and temporary disk space, but also improve performance"/>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/s41592-021-01101-x</citation>
        </citations>
    </xml>
    <xml name="output_macro">
        <data format="txt" name="blast_pairw" label="${tool.name} on ${on_string}: Blast pairwise">
            <filter>output_section["output"]["outfmt"] == "0"</filter>
        </data>
        <data format="xml" name="blast_xml" label="${tool.name} on ${on_string}: Blast XML">
            <filter>output_section["output"]["outfmt"] == "5"</filter>
        </data>
        <data format="tabular" name="blast_tabular" label="${tool.name} on ${on_string}: Blast Tabular">
            <filter>output_section["output"]["outfmt"] == "6"</filter>
        </data>
        <!-- for daa diamond appends the .daa extension -> hence from_work_dir -->
        <data format="daa" name="daa_output" label="${tool.name} on ${on_string}: DAA" from_work_dir="output.daa">
            <filter>output_section["output"]["outfmt"] == "100"</filter>
        </data>
        <data format="sam" name="sam_output" label="${tool.name} on ${on_string}: SAM">
            <filter>output_section["output"]["outfmt"] == "101"</filter>
        </data>
        <data format="tabular" name="tax_output" label="${tool.name} on ${on_string}: Taxonomic classification">
            <filter>output_section["output"]["outfmt"] == "102"</filter>
        </data>
        <data format="json" name="json_output" label="${tool.name} on ${on_string}: Json flat">
            <filter>output_section["output"]["outfmt"] == "104"</filter>
        </data>
    </xml>
    <token name="@OUTPUT_ARGS@">
        #if $output_section.output.outfmt == "0"
            --outfmt '0'
            --out '$blast_pairw'
        #else if $output_section.output.outfmt == "5"
            --outfmt '5'
            --out '$blast_xml'
        #else if $output_section.output.outfmt == "6"
            --outfmt '6' #echo ' '.join(str($output_section.output.fields).split(','))
            --header $output_section.output.header
            --out '$blast_tabular'
        #else if $output_section.output.outfmt == "100"
            --outfmt '100'
            --out output.daa
        #else if $output_section.output.outfmt == "101"
            --outfmt '101'
            --out '$sam_output'
        #else if $output_section.output.outfmt == "102"
            --outfmt '102'
            --out '$tax_output'
            $output_section.output.include_lineage
        #else if $output_section.output.outfmt == "104"
            --outfmt '104' #echo ' '.join(str($output_section.output.fields).split(','))
            --out '$json_output'
        #end if
    </token>
    <token name="@HITFILTER_ARGS@">
        #if str($hit_filter.hit_filter_select) == 'max':
            --max-target-seqs '$hit_filter.max_target_seqs'
        #else:
            --top '$hit_filter.top'
        #end if
    </token>

    <xml name="taxon_cond_macro" tokens="cond_name,label,help,argument">
        <conditional name="@COND_NAME@">
            <param name="tax_select" type="select" label="@LABEL@" help="Any taxonomic rank can be used, and only reference sequences matching one of the specified taxon ids will be searched against.">
                <option value="no" selected="True">No</option>
                <option value="list">List of taxids entered manually</option>
                <option value="file">List of taxids from single column tabular file</option>
            </param>
            <when value="no"/>
            <when value="list">
                <param argument="@ARGUMENT@" type="text" value="" label="Taxon IDss" help="Comma separated list">
                    <validator type="regex" message="Taxonlist needs to be a comma separated list of integers">[0-9,]*</validator>
                </param>
            </when>
            <when value="file">
                <param argument="@ARGUMENT@" type="data" format="tabular" label="Taxon id file" help="One taxon ID per line"/>
            </when>
        </conditional>
    </xml>
</macros>