comparison humann2.xml @ 1:1d6d855c10d8 draft

planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/humann2/ commit 6753a2c0fec9222f5977cab43a855c63fa9f7bee

0:1ab06263e083

        <requirement type="package" version="2.24">rapsearch</requirement>
        <requirement type="package" version="2.7.10">python</requirement>
    </expand>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
        #if $nucleotide_db.nucleotide_db_selector == "history"
            mkdir nucleotide_db
            &&
            #for $file in $nucleotide_db.nucleotide_database:
                cp '$file' 'nucleotide_db/$file.name' &&
            #end for
        #end if

        #if $protein_db.protein_db_selector == "history"
            mkdir protein_db
            &&
            #if $translated_alignment == "diamond"
                diamond makedb
                    --in '$protein_db.protein_database'
                    --db 'protein_db/protein_db'
                    --threads "\${GALAXY_SLOTS:-4}"
            #else
                prerapsearch 
                    -d '$protein_db.protein_database'
                    -n 'protein_db/protein_db'
            #end if
            &&
        #end if

        #if $taxo_profile.taxonomic_profile_test == "false"
            #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
                mkdir ref_db
                &&
                bowtie2-build '$taxo_profile.metaphlan2_db_choice.bowtie2db' 'ref_db/ref_db'
                &&
                python '$__tool_directory__/transform_json_to_pkl.py'
                    --json_input '$taxo_profile.metaphlan2_db_choice.mpa_pkl'
                    --pkl_output 'ref_db/metadata.pkl'
                &&
            #end if
        #end if

        humann2
            --input '$input'
            -o 'output'
            $bypass.bypass_prescreen
            $bypass.bypass_nucleotide_index
            $bypass.bypass_translated_search
            $bypass.bypass_nucleotide_search
            
            #set $metaphlan_option = "-t rel_ab"
            #if $taxo_profile.taxonomic_profile_test == "true":
                --taxonomic-profile '$taxo_profile.taxonomic_profile'
            #else
                #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
                    #set $metaphlan_option += " --bowtie2db " + 'ref_db/ref_db'
                    #set $metaphlan_option += " --mpa_pkl " + 'ref_db/metadata.pkl'
                #else
                    #set $path = $taxo_profile.metaphlan2_db_choice.cached_db.fields.path
                    #set $value = $taxo_profile.metaphlan2_db_choice.cached_db.fields.value
                    #set $metaphlan_option += " --bowtie2db " + $path + "/" + $value
                    #set $metaphlan_option += " --mpa_pkl " + $path + "/" + $value + ".pkl"
                #end if
            #end if
            --metaphlan-options="$metaphlan_option"

            #if $nucleotide_db.nucleotide_db_selector == "cached"
                --nucleotide-database '$nucleotide_db.nucleotide_database.fields.path'
            #else
                --nucleotide-database nucleotide_db
            #end if

            --translated-alignment '$translated_alignment'
            #if $protein_db.protein_db_selector == "cached"
                --protein-database '$protein_db.protein_database.fields.path'
            #else
                --protein-database protein_db
            #end if
            --search-mode '$search_mode'
            --pathways '$pathways' 

            --annotation-gene-index $adv.annotation_gene_index
            --evalue '$adv.evalue'
            --threads "\${GALAXY_SLOTS:-4}"
            --memory-use minimum
	        --prescreen-threshold '$adv.prescreen_threshold'
            --identity-threshold '$adv.identity_threshold'
            --translated-subject-coverage-threshold '$adv.translated_subject_coverage_threshold'
            --translated-query-coverage-threshold '$adv.translated_query_coverage_threshold'
            #if $adv.id_mapping
                --id-mapping '$adv.id_mapping'
            #end if
            --xipe '$adv.xipe'
            --minpath '$adv.minpath'
            --pick-frames '$adv.pick_frames'
            --gap-fill '$adv.gap_fill'
            --output-format '$adv.output_format'
            --output-max-decimals '$adv.output_max_dec'
            --output-basename 'humann2'
            $adv.remove_statified_output
            $adv.remove_column_description_output
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="fastq,fasta,sam,bam,biom1" label="Input sequence file"/>
        <section name="bypass" title="Options to bypass some steps" expanded="False">
            <param name="bypass_prescreen" argument="--bypass-prescreen" type="boolean" checked="false" truevalue="--bypass-prescreen" falsevalue="" label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/>
            <param name="bypass_nucleotide_index" argument="--bypass-nucleotide-index" type="boolean" checked="false" truevalue="--bypass-nucleotide-index" falsevalue="" label="Bypass the nucleotide index step and run on the indexed ChocoPhlAn database?"/>
            <param name="bypass_translated_search" argument="--bypass-translated-search" type="boolean" checked="false" truevalue="--bypass-translated-search" falsevalue="" label="Bypass the translated search step?"/>
            <param name="bypass_nucleotide_search" argument="--bypass-nucleotide-search" type="boolean" checked="false" truevalue="--bypass-translated-search" falsevalue="" label="Bypass the nucleotide search steps?"/>
        </section>
        <conditional name="taxo_profile">
            <param name="taxonomic_profile_test" type="select" label="Use a custom taxonomic profile?" help="The file must have been created by MetaPhlan2">
                <option value="true">Yes</option>
                <option value="false" selected="true">No</option>

            <param argument="--evalue" type="float" value="1" label="E-value threshold to use with the translated search"/>
            <param name="prescreen_threshold" argument="--prescreen-threshold" type="float" value="0.01" label="Minimum percentage of reads matching a species"/>
            <param name="identity_threshold" argument="--identity-threshold" type="float" value="50" label="Identity threshold for alignments"/>
            <param name="translated_subject_coverage_threshold" argument="--translated-subject-coverage-threshold" type="float" value="50" label="Subject coverage threshold for translated alignments"/>
            <param name="translated_query_coverage_threshold" argument="--translated-query-coverage-threshold" type="float" value="50" label="Subject coverage threshold for translated alignments"/>
            <param name="id_mapping" argument="--id-mapping" type="data" format="tsv" label="id mapping file for alignments" optional="True"/>
            <param argument="--xipe" type="boolean" checked="false" truevalue="on" falsevalue="off" label="Use xipe computation?"/>
            <param argument="--minpath" type="boolean" checked="true" truevalue="on" falsevalue="off" label="Use minpath computation?"/>
            <param name="pick_frames" type="boolean" checked="true" truevalue="on" falsevalue="off" label="Use pick frames computation?" argument="--pick-frames"/>
            <param name="gap_fill" type="boolean" checked="true" truevalue="on" falsevalue="off" label="Use gap fill computation?" argument="--gap-fill"/>
            <param name="output_format" type="select" label="Format of the output files" argument="--output-format">
                <option value="tsv" selected="true">TSV</option>
                <option value="biom">BIOM</option>
            </param>
            <param name="output_max_dec" type="integer" value="10" label="Number of decimals to output" argument="--output-max-decimals"/>
            <param name="remove_statified_output" type="boolean" checked="false" truevalue="--remove-stratified-output" falsevalue="" label="Remove stratification from output?" argument="--remove-stratified-output"/>
            <param name="remove_column_description_output" type="boolean" checked="false" truevalue="--remove-column-description-output" falsevalue="" label="Remove stratification from output?" argument="--remove-column-description-output"/>
            
        </section>
    </inputs>
    <outputs>
        <data format="tsv" name="gene_families_tsv" from_work_dir="output/humann2_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >

1:1d6d855c10d8

        <requirement type="package" version="2.24">rapsearch</requirement>
        <requirement type="package" version="2.7.10">python</requirement>
    </expand>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
#if $nucleotide_db.nucleotide_db_selector == "history"
    mkdir nucleotide_db
    &&
    #for $file in $nucleotide_db.nucleotide_database:
        cp '$file' 'nucleotide_db/$file.name' &&
    #end for
#end if

#if $protein_db.protein_db_selector == "history"
    mkdir protein_db
    &&
    #if $translated_alignment == "diamond"
        diamond makedb
            --in '$protein_db.protein_database'
            --db 'protein_db/protein_db'
            --threads "\${GALAXY_SLOTS:-4}"
    #else
        prerapsearch 
            -d '$protein_db.protein_database'
            -n 'protein_db/protein_db'
    #end if
    &&
#end if

#if $taxo_profile.taxonomic_profile_test == "false"
    #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
        mkdir ref_db
        &&
        bowtie2-build '$taxo_profile.metaphlan2_db_choice.bowtie2db' 'ref_db/ref_db'
        &&
        python '$__tool_directory__/transform_json_to_pkl.py'
            --json_input '$taxo_profile.metaphlan2_db_choice.mpa_pkl'
            --pkl_output 'ref_db/metadata.pkl'
        &&
    #end if
#end if

humann2
    --input '$input'
    -o 'output'
    $bypass.bypass_prescreen
    $bypass.bypass_nucleotide_index
    $bypass.bypass_translated_search
    $bypass.bypass_nucleotide_search
    
    #set $metaphlan_option = "-t rel_ab"
    #if $taxo_profile.taxonomic_profile_test == "true":
        --taxonomic-profile '$taxo_profile.taxonomic_profile'
    #else
        #if $taxo_profile.metaphlan2_db_choice.metaphlan2_db_selector == "history"
            #set $metaphlan_option += " --bowtie2db " + 'ref_db/ref_db'
            #set $metaphlan_option += " --mpa_pkl " + 'ref_db/metadata.pkl'
        #else
            #set $path = $taxo_profile.metaphlan2_db_choice.cached_db.fields.path
            #set $value = $taxo_profile.metaphlan2_db_choice.cached_db.fields.value
            #set $metaphlan_option += " --bowtie2db " + $path + "/" + $value
            #set $metaphlan_option += " --mpa_pkl " + $path + "/" + $value + ".pkl"
        #end if
    #end if
    --metaphlan-options="$metaphlan_option"

    #if $nucleotide_db.nucleotide_db_selector == "cached"
        --nucleotide-database '$nucleotide_db.nucleotide_database.fields.path'
    #else
        --nucleotide-database nucleotide_db
    #end if

    --translated-alignment '$translated_alignment'
    #if $protein_db.protein_db_selector == "cached"
        --protein-database '$protein_db.protein_database.fields.path'
    #else
        --protein-database protein_db
    #end if
    --search-mode '$search_mode'
    --pathways '$pathways' 

    --annotation-gene-index $adv.annotation_gene_index
    --evalue '$adv.evalue'
    --threads "\${GALAXY_SLOTS:-4}"
    --memory-use minimum
    --prescreen-threshold '$adv.prescreen_threshold'
    --identity-threshold '$adv.identity_threshold'
    --translated-subject-coverage-threshold '$adv.translated_subject_coverage_threshold'
    --translated-query-coverage-threshold '$adv.translated_query_coverage_threshold'
    #if $adv.id_mapping
        --id-mapping '$adv.id_mapping'
    #end if
    --xipe '$adv.xipe'
    --minpath '$adv.minpath'
    --pick-frames '$adv.pick_frames'
    --gap-fill '$adv.gap_fill'
    --output-format '$adv.output_format'
    --output-max-decimals '$adv.output_max_dec'
    --output-basename 'humann2'
    $adv.remove_statified_output
    $adv.remove_column_description_output
    ]]></command>
    <inputs>
        <param argument="--input" type="data" format="fastq,fasta,sam,bam,biom1" label="Input sequence file"/>
        <section name="bypass" title="Options to bypass some steps" expanded="False">
            <param name="bypass_prescreen" argument="--bypass-prescreen" type="boolean" truevalue="--bypass-prescreen" falsevalue="" checked="false" label="Bypass the prescreen step and run on the full ChocoPhlAn database?"/>
            <param name="bypass_nucleotide_index" argument="--bypass-nucleotide-index" type="boolean" truevalue="--bypass-nucleotide-index" falsevalue="" checked="false" label="Bypass the nucleotide index step and run on the indexed ChocoPhlAn database?"/>
            <param name="bypass_translated_search" argument="--bypass-translated-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the translated search step?"/>
            <param name="bypass_nucleotide_search" argument="--bypass-nucleotide-search" type="boolean" truevalue="--bypass-translated-search" falsevalue="" checked="false" label="Bypass the nucleotide search steps?"/>
        </section>
        <conditional name="taxo_profile">
            <param name="taxonomic_profile_test" type="select" label="Use a custom taxonomic profile?" help="The file must have been created by MetaPhlan2">
                <option value="true">Yes</option>
                <option value="false" selected="true">No</option>

            <param argument="--evalue" type="float" value="1" label="E-value threshold to use with the translated search"/>
            <param name="prescreen_threshold" argument="--prescreen-threshold" type="float" value="0.01" label="Minimum percentage of reads matching a species"/>
            <param name="identity_threshold" argument="--identity-threshold" type="float" value="50" label="Identity threshold for alignments"/>
            <param name="translated_subject_coverage_threshold" argument="--translated-subject-coverage-threshold" type="float" value="50" label="Subject coverage threshold for translated alignments"/>
            <param name="translated_query_coverage_threshold" argument="--translated-query-coverage-threshold" type="float" value="50" label="Subject coverage threshold for translated alignments"/>
            <param name="id_mapping" argument="--id-mapping" type="data" format="tsv" optional="true" label="id mapping file for alignments"/>
            <param argument="--xipe" type="boolean" truevalue="on" falsevalue="off" checked="false" label="Use xipe computation?"/>
            <param argument="--minpath" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use minpath computation?"/>
            <param name="pick_frames" argument="--pick-frames" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use pick frames computation?"/>
            <param name="gap_fill" argument="--gap-fill" type="boolean" truevalue="on" falsevalue="off" checked="true" label="Use gap fill computation?"/>
            <param name="output_format" argument="--output-format" type="select" label="Format of the output files">
                <option value="tsv" selected="true">TSV</option>
                <option value="biom">BIOM</option>
            </param>
            <param name="output_max_dec" argument="--output-max-decimals" type="integer" value="10" label="Number of decimals to output"/>
            <param name="remove_statified_output" argument="--remove-stratified-output" type="boolean" truevalue="--remove-stratified-output" falsevalue="" checked="false" label="Remove stratification from output?"/>
            <param name="remove_column_description_output" argument="--remove-column-description-output" type="boolean" truevalue="--remove-column-description-output" falsevalue="" checked="false" label="Remove stratification from output?"/>
            
        </section>
    </inputs>
    <outputs>
        <data format="tsv" name="gene_families_tsv" from_work_dir="output/humann2_genefamilies.tsv" label="${tool.name} on ${on_string}: Gene families and their abundance" >