view macros.xml @ 0:88fe28c4976d draft

"planemo upload commit 4ee329c2779b2e6e1ea0b58e4c636ff0658a8852-dirty"

<macros>
    <token name="@TOOL_VERSION@">0.1.1</token>
    <xml name="requirements">
        <requirement type="package" version="0.1.1">coast</requirement>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@misc{noauthor_coast_nodate,
                    title = {{COAST} - {Compartive} {Ominc} {Alignment} {Search} {Tool}},
                    url = {https://gitlab.com/coast_tool/COAST},
                    abstract = {Alignment search tool that identifies similar proteomes},
                    language = {en},
                    urldate = {2021-06-22},
                }
            </citation>
        </citations>
    </xml>
    <xml name="input_query">
        <conditional name="query_type">
            <param name="source" type="select" label="Select the type of input file">
                <option value="coast_gb">COAST from GenBank</option>
                <option value="coast_fa">COAST from FASTA</option>
            </param>
            <when value="coast_gb">
                <param name="query_file" type="data" format="GenBank" label="Load a query proteome in Genebank"/>
                <param name="query_key" type="select" label="List the GB file Features to be used as Proteins, do so in a way to prevent duplicated proteins.">
                    <option value="CDS" selected="true">CDS</option>
                    <option value="product">product</option>
                </param>
            </when>
            <when value="coast_fa">
                <param name="query_file" type="data" format="FASTA" label="Load a query proteome in FASTA"/>
            </when>
        </conditional>
    </xml>
    <token name="@QUERY@"><![CDATA[
        "$query_type.query_file"
    ]]></token>
    <token name="@QUERY_KEYWORDS@"><![CDATA[
        #if $query_type.source == 'coast_gb'
            --keywords '$query_type.query_key'
        #end if
    ]]></token>

    <xml name="protein_db">
        <param name="db" type="select" optional="false" label="BLAST-Ready protein sequences database.">
            <options from_data_table="blastdb_p" />
        </param>
    </xml>
    <token name="@DB@"><![CDATA[
        "$db"
    ]]></token>

    <xml name="output_format">
        <param name="outfmt" type="select" optional="true" multiple="true" display="checkboxes" label="Select outputs">
            <option value="b" selected="true">Best Hits</option>
            <option value="a" selected="true">Aggregated Metrics</option>
            <option value="r" selected="true">Report</option>
        </param>
    </xml>
    <token name="@OUTPUT_FORMAT@"><![CDATA[
        #if $outfmt
            --outfmt
            #for $format in $outfmt
                '${format}'
            #end for
        #end if
    ]]></token>
    <token name="@OUTPUT@"><![CDATA[
        --quiet
    ]]></token>

    <xml name="aai_filter">
        <param name="aai" type="integer" value="10" label="AAIc filtering score"/>
        <param name="min_cov" type="integer" value="50" label="Minimum Coverage for AAIbd hit selection"/>
        <param name="min_id" type="integer" value="40" label="Minimum Amino Acid Identity for AAIbd hit selection"/>
    </xml>
    <token name="@AAI_FILTER@"><![CDATA[
        --aai '$aai'
        --cov '$min_cov'
        --id '$min_id'
    ]]></token>

    <xml name="hypothetical_filter">
        <param name="hypothetical" type="boolean" checked="false" label="Filter hypothetical proteins from query. Read description for more information." truevalue="--filter_hypothetical" falsevalue=""/>
    </xml>
    <token name="@HYPO_FILTER@"><![CDATA[
        #if $hypothetical
            '$hypothetical'
        #end if
    ]]></token>

    <xml name="results_alignment">
        <data format_source="tabular" format="tabular" name="blast_results" label="COAST - Batch alignment results" from_work_dir="blast_results.tab"/>
    </xml>

    <xml name="results_report">
        <data format_source="html"  format="html" name="coast_report" label="COAST - Summarized report" from_work_dir="coast_report.html">
            <filter>"r" in outfmt</filter>
        </data>
        <data format_source="tabular" format="tabular" label="COAST - Best-hits table" name="bh_results" from_work_dir="bh_results.tab">
            <filter>"b" in outfmt</filter>
        </data>
        <data format_source="tabular" format="tabular" label="COAST - Results table" name="coast_results" from_work_dir="coast_results.tab">
            <filter>"a" in outfmt</filter>
        </data>
    </xml>

    <xml name="blast_taxon_filter">
        <conditional name="filter_type">
            <param name="taxon_filter_type" type="select" label="Type of taxonomic filter">
                <option value="taxidlist_dm">Pre-defined taxonomic filters</option>
                <option value="taxidlist_user">User-provided file based list</option>
                <option value="taxonlist">Comma separated list</option>
            </param>
            <when value="taxidlist_dm">
                <param name="taxidlist" type="select" optional="true" label="Select pre-defined taxonomic filters">
                    <options from_data_table="coast_taxonomic_filters" />
                </param>
            </when>
            <when value="taxidlist_user">
                <param name="taxidlist" type="data" format="txt" optional="true" label="Load file with filtering taxids."/>
            </when>
            <when value="taxonlist">
                <param name="taxonlist" type="text" optional="true" label="Comma separated list of TAXIDs nodes, ranking species or lower"/>
            </when>
        </conditional>
    </xml>
    <token name="@BLAST_TAX_FILTER@"><![CDATA[
        #if $filter_type.taxon_filter_type == "taxidlist_dm"
            --taxidlist '$filter_type.taxidlist.fields.path'
        #end if
        #if $filter_type.taxon_filter_type == "taxidlist_user"
            --taxidlist '$filter_type.taxidlist'
        #end if
        #if $filter_type.taxon_filter_type == "taxonlist"
            --taxonlist '$filter_type.taxonlist'
        #end if
    ]]></token>

    <xml name="diamond_taxon_filter">
        <conditional name="filter_type">
            <param name="taxon_filter_type" type="select" label="Type of taxonomic filter">
                <option value="taxonlist_pre_defined">Pre-defined taxonomic filters</option>
                <option value="taxonlist">Comma separated list</option>
            </param>
        <when value="taxonlist_pre_defined">
            <param name="taxonlist" type="select" optional="true" label="Select pre-defined taxonomic filters">
                <option value="10239">Viruses - 102239</option>
                <option value="2157">Archaea - 2157</option>
                <option value="2">Bacteria - 2</option>
            </param>
        </when>
        <when value="taxonlist">
            <param name="taxonlist" type="text" optional="true" label="Comma separated list of TAXIDs nodes, ranking species or lower"/>
        </when>
        </conditional>
    </xml>
    <token name="@DIAMOND_TAX_FILTER@"><![CDATA[
        #if $taxonlist
            --taxonlist '$taxonlist'
        #end if
    ]]></token>

    <xml name="generic_aln_options">
        <param name="threshold_no" type="integer" optional="true" label="E-Value Threshold"/>
        <param name="scoring_matrix" type="select" optional="true" label="Scoring matrix">
            <option value="BLOSUM45">BLOSUM45</option>
            <option value="BLOSUM50">BLOSUM50</option>
            <option value="BLOSUM62">BLOSUM62</option>
            <option value="BLOSUM80">BLOSUM80</option>
            <option value="BLOSUM90">BLOSUM90</option>
            <option value="PAM250">PAM250</option>
            <option value="PAM70">PAM70</option>
            <option value="PAM30">PAM30</option>
        </param>
        <param name="gap_open" type="integer" optional="true" label="Gap opening penalty"/>
        <param name="gap_ext" type="integer" optional="true" label="Gap extension penalty"/>
    </xml>
    <token name="@GENERIC_ALN_OPTIONS@"><![CDATA[
        #if $aln_adv.scoring_matrix
            --matrix '$aln_adv.scoring_matrix'
        #end if
        #if $aln_adv.threshold_no
            --evalue '$aln_adv.threshold_no'
        #end if
        #if $aln_adv.gap_open
            --gapopen '$aln_adv.gap_open'
        #end if
        #if $aln_adv.gap_ext
            --gapextend '$aln_adv.gap_ext'
        #end if
    ]]></token>

    <xml name="blast_aln_options">
        <param name="task" type="select" optional="true" label="Type of BLAST">
            <option value="blast">blast</option>
            <option value="blastp-fast">blastp-fast</option>
            <option value="blastp-short">blastp-short</option>
        </param>
    </xml>
    <token name="@BLAST_ALN_OPTIONS@"><![CDATA[
        #if $aln_adv.task
            --task '$aln_adv.task'
        #end if
    ]]></token>

    <xml name="diamond_aln_options">
        <param name="diamond_sens" type="select" label="Select the desired sensibility">
            <option value="sensitive" selected="true">sensitive</option>
            <option value="more-sensitive">more sensitive</option>
            <option value="very-sensitive">very sensitive</option>
            <option value="ultra-sensitive">ultra sensitive</option>
        </param>
    </xml>
    <token name="@DIAMOND_ALN_OPTIONS@"><![CDATA[
        #if $aln_adv.diamond_sens
            --sens '$aln_adv.diamond_sens'
        #end if
    ]]></token>

    <xml name="merlin_db_selection">
        <param name="db" type="select" label="Select the desired database">
            <option value="UniProtKB_SwissProt">SwissProt</option>
            <option value="UniProtKB_Trembl">Trembl</option>
        </param>
    </xml>
</macros>