annotate picrust2_functions_macros.xml @ 0:c5fd7b97c2a4 draft default tip

planemo upload for repository https://github.com/geraldinepascal/FROGS-wrappers/ commit 78ca62b54aee22893d278d9c3d495527be405f8a

<?xml version="1.0"?>
<macros>
    <token name="@PICRUST2_FUNCTIONS_CMD_LINE@">
        frogsfunc_functions.py
                @CPUS@
                --input-biom '$input_biom'
                --input-fasta '$input_fasta'
                --input-tree '$input_tree'
                --input-marker-copy '$input_marker_copy'
                --marker-type $marker.value

                #if $marker.value == "16S"
                    --functions ${" ".join(str($functions).split(","))}
                #end if

                #if $marker.value != "16S"
                    --input-function-table $functions.fields.fun
                #end if 

                --max-nsti $max_nsti
                --min-blast-ident $min_blast_ident
                --min-blast-cov $min_blast_cov
                --hsp-method '$hsp_method'

                --html '$html'
                --output-excluded '$output_excluded'
                --output-biom '$output_biom'
                --output-fasta '$output_fasta'
                --output-asv-copy-norm '$output_asv_norm'
                --output-weighted-nsti '$output_weighted_nsti'
                --prefix-function-abund unstrat_abundance
    </token>

    <xml name="picrust2_functions_inputs">
        <!-- Files -->
        <param argument="--input-biom" format="biom1" type="data" label="ASV abundance file (format Biom)" help="ASV biom abundance file containing the PICRUSt2 taxonomic annotation (output of picrust2_placeseq_and_copynumber tool)." />
        <param argument="--input-fasta" type="data" format="fasta" label="Sequence file (format: FASTA)" help="ASV sequence fasta file." />
        <param argument="--input-tree" format="nhx,newick" type="data" label="ASV Phylogenetic tree (format nhx,newick)" help="PICRUSt2 phylogenetic tree."/>
        <param argument="--input-marker-copy" format="tsv" type="data" label="Marker copy number file (format TSV)" help="PICRUSt2 estimation of marker copy number."/>
        
        <!-- Parameters-->
        <param name="marker" type="select" multiple="false" display="radio" label="Marker gene" help="Marker gene analysed.">
            <options from_data_table="frogs_picrust2_functions">
                <column name='name' index='0' />
                <column name='value' index='0' />
                <filter type="unique_value" column='0'/>
                <validator type="no_options" message="A built-in database is not available" />
            </options>
        </param>
        <param argument="--functions" type="select" label="Target function database" multiple="true" optional="false" help=" 16S : at least 'EC' or/and 'KO' should be chosen (EC for Metacyc pathway analysis or/and KO for KEGG pathway analysis) - others values are optionnal. ITS and 18S : 'EC' only available." >
            <options from_data_table="frogs_picrust2_functions">
                <column name='name' index='1' />
                <column name='value' index='1' />
                <column name='path' index='2' />
                <column name='fun' index='3' />
                <filter type="param_value" ref="marker" column="0" />              
            </options>
        </param>
        <param argument="--max-nsti" type="float" label="NSTI cut-off" help="ASV sequence with NSTI above this threshold will be excluded. (default: 2)" value="2" min="0" optional="false" />
        <param argument="--min-blast-ident" type="float" label="Identity alignment cut-off" help="Percentage identity between the ASV sequence and the closest PICRUSt2 reference sequence. ASV sequence with identity percentage bellow this threshold will be excluded. (default: None)" value="0" min="0" max="1" optional="true" />
        <param argument="--min-blast-cov" type="float" label="Coverage alignment cut-off" help="Coverage identity of the alignment between the input sequence and the PICRUSt2 reference sequence. ASV sequence with coverage percentage bellow this threshold will be excluded. (default: None)" value="0" min="0" max="1" optional="true" />
        <param argument="--hsp-method" type="select" label="HSP method" help="Hidden-state prediction method to use: maximum parsimony (mp), empirical probabilities (emp_prob), continuous traits prediction using subtree averaging (subtree_average), continuous traits prediction with phylogentic independent contrast (pic), continuous traits reconstruction using squared-change parsimony (scp) (default: mp)." multiple="false" display="radio">
            <option value="mp">mp</option>
            <option value="emp_prob">emp_prob</option>
            <option value="pic">pic</option>
            <option value="scp">scp</option>
            <option value="subtree_average">subtree_average</option>
        </param>
    </xml>

    <!-- Test -->
    <xml name="picrust2_functions_test_input">
        <param name="input_fasta" value="references/25-frogsfunc_placeseqs.fasta" />
        <param name="input_biom" value="references/25-frogsfunc_placeseqs.biom" />
        <param name="input_tree" value="references/25-frogsfunc_placeseqs_tree.nwk" />
        <param name="input_marker_copy" value="references/25-frogsfunc_placeseqs_marker.tsv" />

        <!-- Parameters -->
        <param name="marker" value="16S" />
        <param name="functions" value="EC" />
        <param name="max_nsti" value="2" />
    </xml>

    <xml name="picrust2_functions_test_output">
        <output name="html" file="references/26-frogsfunc_functions_summary.html" compare="diff" lines_diff="0" />
        <output name="output_excluded" file="references/26-frogsfunc_functions_excluded.tsv" compare="diff" lines_diff="0" />
        <output name="output_biom" file="references/26-frogsfunc_functions.biom" compare="diff" lines_diff="0" />
        <output name="output_fasta" file="references/26-frogsfunc_functions.fasta" compare="diff" lines_diff="0" />
        <output name="output_asv_norm" file="references/26-frogsfunc_functions_marker_norm.tsv" compare="diff" lines_diff="0" />
        <output name="output_weighted_nsti" file="references/26-frogsfunc_functions_weighted_nsti.tsv" compare="diff" lines_diff="0" />
        <output name="output_function_ec_abund" file="references/26-frogsfunc_functions_unstrat_EC.tsv" compare="diff" lines_diff="0" />
        <output name="output_copy_ec_abund" file="references/EC_copynumbers_predicted.tsv" compare="diff" lines_diff="0" />
    </xml>   
</macros>