view macros.xml @ 4:80ce9ca55697 draft

planemo upload commit d27827cf38d30b9c98923f73bc9cae4ffe41361b

<macros>
    <token name="@VERSION@">0.99.2</token>
    <xml name="requirements">
        <requirements>
        <requirement type="package" version="@VERSION@">metaquantome</requirement>
            <yield/>
        </requirements>
    </xml>
    <xml name="ONTOLOGY_ARGS">
        <conditional name="ontology_args">
            <param name="ontology" type="select" label="Ontology">
                <option value="go">Gene Ontology (GO terms)</option>
                <option value="ec">Enzyme Commission (EC) numbers</option>
                <option value="cog">Clusters of Orthologous Groups (COG categories)</option>
            </param>
            <when value="go">
                <param argument="--slim_down" type="boolean" label="Use slim GO"/>
            </when>
            <when value="ec">
                <!-- do nothing -->
            </when>
            <when value="cog">
                <!-- do nothing -->
            </when>
        </conditional>
    </xml>
    <xml name="FUNC_FILE">
        <param argument="--func_file" type="data" format="tabular" label="Functional file"
            help="Tabular file with a peptide sequence column and a functional assignment column for GO-term, EC number, or COG."/>
        <param argument="--pep_colname_func" type="text" label="Peptide column name"
            help="The column name within the function file that corresponds to the peptide sequences">
            <validator type="empty_field"/>
        </param>
        <param argument="--func_colname" type="text" label="Functional column name"
            help="The column name within the function file with the functional terms">
            <validator type="empty_field"/>
        </param>
    </xml>
    <xml name="TAX_FILE">
        <param argument="--tax_file" type="data" format="tabular" label="Taxonomy assignments file"/>
        <param argument="--pep_colname_tax" type="text" label="Peptide column name"
            help="The column name within the taxonomy file that corresponds to the peptide sequences">
            <validator type="empty_field"/>
        </param>
        <param argument="--tax_colname" type="text" label="Taxonomy column name">
            <help>
                Name of taxonomy column in taxonomy assignments file. The column must
                be either NCBI taxids (strongly preferred) or taxonomy
                names. Unipept name output is known to function well,
                but other formats may not work.
            </help>
            <validator type="empty_field"/>
        </param>
    </xml>
    <token name="@MAKE_SAMPS_TSV@"><![CDATA[
        ### make samps config file
        #if $samps_args.samps_src == 'history':
            cat '$samps_args.samps_file' > samp_file.tab &&
        #else:
            #set $samp_header = 'group\tcolnames'
            echo -e '${samp_header}' > samp_file.tab &&
            #for $s in $samps_args.samps
                #set $sample = str($s.group_name) + '\t' + str($s.col_names)
                echo -e '${sample}' >> samp_file.tab &&
            #end for
        #end if
    ]]>
    </token>
    <token name="@DB_DIR@"><![CDATA[
        #if $db_dir.db_loc == 'auto':
            #if $mode_args.mode == 'ft'
                --ft_func_data_dir data
                --ft_tax_data_dir  data
            #else
                --data_dir data
            #end if
        ## #elif $db_dir.db_loc == 'cached':
        #end if
    ]]>
    </token>
    <xml name="data_dir">
        <conditional name="db_dir">
            <param argument="db_loc" type="select" label="Taxonomy and Functional Databases">
                <option value="auto">automatically load databases</option>
                <!-- bioconda recipe would need to install the databases
                <option value="pkg">use default metaquantome databases (not current)</option>
                -->
                <!-- requires a data_manager
                <option value="cached">Use cached databases</option>
                -->
            </param>
            <when value="auto"/>
            <!-- bioconda recipe would need to install the databases
            <when value="pkg"/>
            -->
            <!-- requires a data_manager
            <when value="cached">
            </when>
            -->
        </conditional>
    </xml>
    <token name="@COMMON_PARAMS@"><![CDATA[
            --samps samp_file.tab
            --mode '$mode_args.mode'
            #if $mode_args.mode == 'f'
                --ontology='$mode_args.ontology_args.ontology'
                #if $mode_args.ontology_args.ontology == 'go'
                    #if $mode_args.ontology_args.slim_down
                        --slim_down
                    #end if
                #end if
            #end if
            #if $mode_args.mode == 'ft'
                --ontology='$mode_args.ontology_args.ontology'
                #if $mode_args.ontology_args.ontology == 'go'
                    #if $mode_args.ontology_args.slim_down
                        --slim_down
                    #end if
                #end if
            #end if
    ]]>
    </token>
    <token name="@EXPAND_PARAMS@"><![CDATA[
            --samps samp_file.tab
            --mode '$mode_args.mode'
            #if $mode_args.mode == 'f'
                --func_file='$mode_args.func_file'
                --func_colname='$mode_args.func_colname'
                --pep_colname_func='$mode_args.pep_colname_func'
                --ontology='$mode_args.ontology_args.ontology'
                #if $mode_args.ontology_args.ontology == 'go'
                    #if $mode_args.ontology_args.slim_down
                        --slim_down
                    #end if
                #end if
            #end if
            #if $mode_args.mode =='t'
                --tax_file='$mode_args.tax_file'
                --tax_colname='$mode_args.tax_colname'
                --pep_colname_tax='$mode_args.pep_colname_tax'
            #end if
            #if $mode_args.mode == 'ft'
                --func_file='$mode_args.func_file'
                --func_colname='$mode_args.func_colname'
                --pep_colname_func='$mode_args.pep_colname_func'
                --ontology='$mode_args.ontology_args.ontology'
                #if $mode_args.ontology_args.ontology == 'go'
                    #if $mode_args.ontology_args.slim_down
                        --slim_down
                    #end if
                #end if
                --tax_file='$mode_args.tax_file'
                --tax_colname='$mode_args.tax_colname'
                --pep_colname_tax='$mode_args.pep_colname_tax'
                --ft_tar_rank='$mode_args.ft_tar_rank'
            #end if
    ]]>
    </token>

    <xml name="SAMPS">
        <conditional name="samps_args">
            <param argument="samps_src" type="select" label="Samples">
                <option value="history">Use a samples dataset from your history</option>
                <option value="build">Specify samples</option>
            </param>
            <when value="history">
                <param name="samps_file" type="data" format="tabular" label="Samples file">
                </param>
            </when>
            <when value="build">
                <repeat name="samps" title="Samples">
                    <param name="group_name" type="text" label="Group name"/>
                    <param name="col_names" type="text" label="Column names of samples in group"/>
                </repeat>
            </when>
        </conditional>
    </xml>
    <xml name="common_params">
        <conditional name="mode_args">
            <param argument="--mode" type="select" label="Mode">
                <option value="f">Functional analysis</option>
                <option value="t">Taxonomic analysis</option>
                <option value="ft">Functional-taxonomic interaction analysis</option>
            </param>
            <when value="f">
                <expand macro="ONTOLOGY_ARGS"/>
            </when>
            <when value="t">
            </when>
            <when value="ft">
                <expand macro="ONTOLOGY_ARGS"/>
            </when>
        </conditional>
        <expand macro="SAMPS"/>
    </xml>
    <xml name="expand_params">
        <conditional name="mode_args">
            <param argument="--mode" type="select" label="Mode">
                <option value="f">Functional analysis</option>
                <option value="t">Taxonomic analysis</option>
                <option value="ft">Functional-taxonomic interaction analysis</option>
            </param>
            <when value="f">
                <expand macro="FUNC_FILE"/>
                <expand macro="ONTOLOGY_ARGS"/>
            </when>
            <when value="t">
                <expand macro="TAX_FILE"/>
            </when>
            <when value="ft">
                <expand macro="FUNC_FILE"/>
                <expand macro="ONTOLOGY_ARGS"/>
                <expand macro="TAX_FILE"/>
                <param argument="--ft_tar_rank" type="select" label="rank at which to group taxonomy">
                    <option value="species">species</option>
                    <option value="genus" selected="true">genus</option>
                    <option value="family">family</option>
                    <option value="order">order</option>
                    <option value="class">class</option>
                    <option value="phylum">phylum</option>
                    <option value="kingdom">kingdom</option>
                </param>
            </when>
        </conditional>
        <expand macro="SAMPS"/>
    </xml>

    <xml name="output_samples_choice">
        <param name="output_samps" type="boolean" truevalue="yes" falsevalue="no" checked="false" label="Output the samples fiile"/>
    </xml>
    <xml name="output_samples">
        <data format="tabular" name="samples_file" label="${tool.name} on ${on_string} samples" from_work_dir="samp_file.tab">
            <filter>output_samps == True</filter>
        </data>
    </xml>

    <xml name="citations">
        <citations>
            <yield />
        </citations>
    </xml>
</macros>