annotate frogs_func_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="@TOOL_VERSION@">5.1.0</token>
    <token name="@VERSION_SUFFIX@">0</token>

    <xml name="frogs_func_requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">frogs</requirement>
            <requirement type="package" version="2.5.1">picrust2</requirement>
            <requirement type="package" version="3.1.1">ete3</requirement>
            <requirement type="package" version="4.5.2">dendropy</requirement>
            <yield />
        </requirements>
    </xml>

    <token name="@CPUS@">--nb-cpus \${GALAXY_SLOTS:-1}</token>
    
    <xml name="frogs_func_outputs">
        <!-- HTML report -->
        <data format="html" name="html" label="${tool.name} - ${tool_name}: report.html" />
        <!-- ASV excluded : all but pathway -->
        <data format="tsv" name="output_excluded" label="${tool.name} - ${tool_name}: ASV_excluded.tsv">
            <filter> frogs_func_tools['tool_name'] != 'picrust2_pathways' </filter>
        </data>
        <data format="biom1" name="output_biom" label="${tool.name} - ${tool_name}: kept_ASV_abundance.biom">
            <filter> frogs_func_tools['tool_name'] != 'picrust2_pathways'  </filter>
        </data>
        <data format="fasta" name="output_fasta" label="${tool.name} - ${tool_name}: kept_ASV_sequences.fasta">
            <filter> frogs_func_tools['tool_name'] != 'picrust2_pathways' </filter>
        </data>
        <!-- Specific picrust2_placeseq_and_copynumber -->
        <data format="tsv" name="output_closests_ref" label="${tool.name} - ${tool_name}: ASV_closests_ref.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_placeseq_and_copynumber' </filter>
        </data>
        <data format="tsv" name="output_marker_copy" label="${tool.name} - ${tool_name}: marker_copy_number_per_ASV.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_placeseq_and_copynumber' </filter>
        </data>
        <data format="newick" name="output_tree" label="${tool.name} - ${tool_name}: ASV_tree.nwk">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_placeseq_and_copynumber' </filter>
        </data>
        <!-- Specific picrust2_functions -->
        <data format="tsv" name="output_asv_norm" label="${tool.name} - ${tool_name}: ASV_abundance_norm.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' </filter>
        </data> 
        <data format="tsv" name="output_weighted_nsti" label="${tool.name} - ${tool_name}: sample_weighted_nsti.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' </filter>
        </data> 
            <!-- By database Function copy number and unstrat abundance-->
                <!-- EC-->
        <data format="tsv" name="output_copy_ec_abund" label="${tool.name} - ${tool_name}: EC_predicted_copy_numbers.tsv" from_work_dir="EC_copynumbers_predicted.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' and "EC" in frogs_func_tools['functions'] </filter>
        </data>
        <data format="tsv" name="output_function_ec_abund" label="${tool.name} - ${tool_name}: EC_unstrat_abundance.tsv" from_work_dir="unstrat_abundance_EC.tsv">
            <filter>frogs_func_tools['tool_name'] == 'picrust2_functions' and "EC" in frogs_func_tools['functions'] </filter>
        </data>
            <!-- KO-->
        <data format="tsv" name="output_copy_ko_abund" label="${tool.name} - ${tool_name}: KO_predicted_copy_numbers.tsv" from_work_dir="KO_copynumbers_predicted.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' and "KO" in frogs_func_tools['functions'] </filter>
        </data>
        <data format="tsv" name="output_function_ko_abund" label="${tool.name} - ${tool_name}: KO_unstrat_abundance.tsv" from_work_dir="unstrat_abundance_KO.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' and "KO" in frogs_func_tools['functions'] </filter>
        </data>
            <!-- PFAM-->
        <data format="tsv" name="output_copy_pfam_abund" label="${tool.name} - ${tool_name}: PFAM_predicted_copy_numbers.tsv" from_work_dir="PFAM_copynumbers_predicted.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' and "PFAM" in frogs_func_tools['functions'] </filter>
        </data>
        <data format="tsv" name="output_function_pfam_abund" label="${tool.name} - ${tool_name}: PFAM_unstrat_abundance.tsv" from_work_dir="unstrat_abundance_PFAM.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' and "PFAM" in frogs_func_tools['functions'] </filter>
        </data>
            <!-- COG-->
        <data format="tsv" name="output_copy_cog_abund" label="${tool.name} - ${tool_name}: COG_predicted_copy_numbers.tsv" from_work_dir="COG_copynumbers_predicted.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' and "COG" in frogs_func_tools['functions'] </filter>
        </data>
        <data format="tsv" name="output_function_cog_abund" label="${tool.name} - ${tool_name}: COG_unstrat_abundance.tsv" from_work_dir="unstrat_abundance_COG.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' and "COG" in frogs_func_tools['functions'] </filter>
        </data>
            <!-- TIGRFAM-->
        <data format="tsv" name="output_copy_tigrfam_abund" label="${tool.name} - ${tool_name}: TIGRFAM_predicted_copy_numbers.tsv" from_work_dir="TIGRFAM_copynumbers_predicted.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' and "TIGRFAM" in frogs_func_tools['functions'] </filter>
        </data>
        <data format="tsv" name="output_function_tigrfam_abund" label="${tool.name} - ${tool_name}: TIGRFAM_unstrat_abundance.tsv" from_work_dir="unstrat_abundance_TIGRFAM.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' and "TIGRFAM" in frogs_func_tools['functions'] </filter>
        </data>
            <!-- PHENO-->
        <data format="tsv" name="output_copy_pheno_abund" label="${tool.name} - ${tool_name}: PHENO_predicted_copy_numbers.tsv" from_work_dir="PHENO_copynumbers_predicted.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' and "PHENO" in frogs_func_tools['functions'] </filter>
        </data>
        <data format="tsv" name="output_function_pheno_abund" label="${tool.name} - ${tool_name}: PHENO_unstrat_abundance.tsv" from_work_dir="unstrat_abundance_PHENO.tsv">
            <filter> frogs_func_tools['tool_name'] == 'picrust2_functions' and "PHENO" in frogs_func_tools['functions'] </filter>
        </data>
        <!-- Specific picrust2_pathways -->
        <!-- <data format="tsv" name="output_pathways_abund" label="${tool.name} - ${tool_name}: ${database}_unstrat_abundance.tsv" from_work_dir="frogsfunc_pathways_unstrat.tsv" >
            <filter> frogs_func_tools['tool_name'] == 'picrust2_pathways' </filter>
        </data> -->
        <data format="tsv" name="output_pathways_abund" label="${tool.name} - ${tool_name}: ${database}_unstrat_abundance.tsv" >
            <filter> frogs_func_tools['tool_name'] == 'picrust2_pathways' </filter>
        </data>
    </xml>
</macros>