comparison assign_taxonomy.xml @ 3:ec3c4654eacc draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/qiime/ commit a831282140ce160035a4ce984f48cc20198ed0a1

2:70206002b220

    <description>to each sequence</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2.0.2">rdptools</requirement>
        <requirement type="package" version="2.2.22">blast-legacy</requirement>
        <requirement type="package" version="2.3.4">vsearch</requirement>
        <requirement type="package" version="1.36.1">mothur</requirement>
    </expand>
    <version_command>assign_taxonomy.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        assign_taxonomy.py
            --input_fasta_fp '$input_fasta_fp'
            #if $id_to_taxonomy_fp
                --id_to_taxonomy_fp '$id_to_taxonomy_fp'
            #end if
            --assignment_method '$methodcond.assignment_method'
            #if $methodcond.assignment_method == "uclust"
                --min_consensus_fraction '$methodcond.min_consensus_fraction'
                --similarity '$methodcond.similarity'
                --uclust_max_accepts '$methodcond.uclust_max_accepts'
            #else if $methodcond.assignment_method == "rdp"
                #if $methodcond.reference_seqs_fp
                    --reference_seqs_fp '$methodcond.reference_seqs_fp'
                #end if
                --confidence '$methodcond.confidence'
            #else if $methodcond.assignment_method == "blast"
                --reference_seqs_fp '$methodcond.reference_seqs_fp'
                --blast_e_value '$methodcond.blast_e_value'
            #else if $methodcond.assignment_method == "rtax"
                --read_1_seqs_fp '$methodcond.read_1_seqs_fp'
                --read_2_seqs_fp '$methodcond.read_2_seqs_fp'
                $methodcond.single_ok
                $methodcond.no_single_ok_generic
                --read_id_regex '$methodcond.read_id_regex'
                --amplicon_id_regex '$methodcond.amplicon_id_regex'
                --header_id_rege '$methodcond.header_id_regex'
            #else if $methodcond.assignment_method == "mothur"
                --confidence '$methodcond.confidence'
            #else if $methodcond.assignment_method == "sortmerna"
                --sortmerna_threads \${GALAXY_SLOTS:-1}
                #if $methodcond.sortmerna_db
                    --sortmerna_db '$methodcond.sortmerna_db'

            #end if
            -o assign_taxonomy
    ]]></command>
    <inputs>
        <param argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file" />
        <param argument="--id_to_taxonomy_fp" label="Tab-delimited file mapping sequences to assigned taxonomy"  type="data" format="tabular" help="Each assigned taxonomy is provided as a semicolon-separated list. For assignment with rdp, each assigned taxonomy must be exactly 6 levels deep" optional="True"/>
        <conditional name="methodcond">
            <param argument="--assignment_method" label="Taxon assignment method" type="select">
                <option selected="True" value="uclust">uclust</option>
                <!--<option value="rdp">rdp</option>
                <option value="blast">blast</option>
                <option value="rtax">rtax</option>
                <option value="mothur">mothur</option>
                <option value="sortmerna">sortmerna</option>-->
            </param>
            <when value="uclust">
                <param argument="--min_consensus_fraction" type="float" value="0.51" label="Minimum fraction of database hits that must have a specific taxonomic assignment to assign that taxonomy to a query"/>
                <param argument="--similarity" type="float" value="0.9" label="Minimum percent similarity (expressed as a fraction between 0 and 1) to consider a database match a hit"/>
                <param argument="uclust_max_accepts" type="integer" value="3" label="Number of database hits to consider when making an assignment"/>
            </when>
            <when value="rdp">
                <param argument="--reference_seqs_fp" label="Reference sequences used as training sequences for the classifier" type="data" format="fasta" optional="True"/>
                <param argument="--confidence" type="float" value="0.5" label="Minimum confidence to record an assignment"/>
            </when>
            <when value="blast">
                <param argument="--reference_seqs_fp" label="Reference sequences used to generate a blast database" type="data" format="fasta" optional="True"/>
                <param argument="--blast_e_value" type="float" value="0.001" label="Maximum e-value to record an assignment"/>
            </when>
            <when value="rtax">
                <param argument="--read_1_seqs_fp" type="data" format="fasta" label="First reads from paired-end sequencing, prior to OTU clustering" help="This file is the result of split_illumina_fastq"/>
                <param argument="--read_2_seqs_fp" type="data" format="fasta" label="Second reads from paired-end sequencing, prior to OTU clustering" help="This file is the result of split_illumina_fastq"/>

                <param argument="--read_id_regex" type="text" value="\S+\s+(\S+)" label="Regex used to parse the result of OTU clustering, to get the read_1_id for each clusterID" help="The clusterID itself is assumed to be the first field, and is not captured by the regex"/>
                <param argument="--amplicon_id_regex" type="text" value="(\S+)\s+(\S+?)\/" label="Regex used to parse the result of split_libraries, to get the ampliconID for each read_1_id" help="Two groups capture read_1_id and ampliconID,  respectively."/>
                <param argument="--header_id_regex" type="text" value="\S+\s+(\S+?)\/" label="Regex used to parse the result of split_libraries, to get the portion of the header that RTAX uses to match mate pairs" help="The default uses the amplicon ID, not including /1 or /3, as the primary key for the query sequences. Typically this regex will be the same as amplicon_id_regex, except that only the second group is captured" />
            </when>
            <when value="mothur">
                <param argument="--confidence" type="float" value="0.5" label="Minimum confidence to record an assignment"/>
            </when>
            <when value="sortmerna">
                <param argument="--sortmerna_db" type="data" format="fasta" label="Pre-existing database to search against" optional="True"/>
                <param argument="--min_consensus_fraction" type="float" value="0.51" label="Minimum fraction of database hits that must have a specific taxonomic assignment to assign that taxonomy to a query"/>
                <param argument="--similarity" type="float" value="0.9" label="Minimum percent similarity (expressed as a fraction between 0 and 1) to consider a database match a hit"/>
                <param argument="--sortmerna_e_value" type="float" value="1.0" label="Maximum E-value when clustering"/>
                <param argument="--sortmerna_coverage" type="float" value="0.9" label="Mininum percent query coverage (of an alignment) to consider a hit, expressed as a fraction between 0 and 1"/>
                <param argument="--sortmerna_best_N_alignments" type="integer" value="5" label="Number best alignments per read to be written"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="log" format="txt" from_work_dir="assign_taxonomy/*_assignments.log" label="${tool.name} on ${on_string}: Log"/>
        <data name="tax_assignments" format="txt" from_work_dir="assign_taxonomy/*.txt" label="${tool.name} on ${on_string}: Taxonomic assignment"/>
        <data name="sortmerna_map" format="tabular" from_work_dir="assign_taxonomy/sortmerna_map.blast" label="${tool.name} on ${on_string}: SortMeRNA Blast">
            <filter>methodcond['assignment_method']=="sortmerna"</filter>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_fasta_fp" value="assign_taxonomy/uclust_input_seqs.fasta"/>
            <param name="assignment_method" value="uclust"/>
            <param name="min_consensus_fraction" value="0.51"/>
            <param name="similarity" value="0.9"/>
            <param name="uclust_max_accepts" value="3" />
            <output name="tax_assignments" value="assign_taxonomy/uclust_taxonomic_assignation.txt"/>
            <output name="log">
                <assert_contents>
                    <has_text text="UclustConsensusTaxonAssigner" />
                    <has_text text="2751331" />
                </assert_contents>
            </output>
        </test>
        <!--<test>
            <param name="input_fasta_fp" value="assign_taxonomy/mothur_ref_seq_set.fna"/>
            <param name="assignment_method" value="sortmerna"/>
            <param name="min_consensus_fraction" value="0.51" />
            <param name="similarity" value="0.9" />
            <param name="sortmerna_e_value" value="1.0" />
            <param name="sortmerna_coverage" value="0.9" />
            <param name="sortmerna_best_N_alignments" value="5" />
            <output name="log">
                <assert_contents>
                    <has_text text="Application:SortMeRNA" />
                    <has_text text="min_consensus_fraction" />
                </assert_contents>
            </output>
            <output name="tax_assignments" value="assign_taxonomy/sortmerna_taxonomic_assignation.txt"/>
            <output name="sortmerna_map" value="assign_taxonomy/sortmerna_map.blast"/>
        </test>-->
    </tests>
    <help><![CDATA[
**What it does**

3:ec3c4654eacc

    <description>to each sequence</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <!--<requirement type="package" version="2.0.2">rdptools</requirement>-->
        <requirement type="package" version="2.2.22">blast-legacy</requirement>
        <requirement type="package" version="2.3.4">vsearch</requirement>
        <requirement type="package" version="1.36.1">mothur</requirement>
    </expand>
    <version_command>assign_taxonomy.py --version</version_command>
    <command detect_errors="aggressive"><![CDATA[
        assign_taxonomy.py
            --input_fasta_fp '$input_fasta_fp'
            #if $id_to_taxonomy_condition.source_selector == 'history'
                --id_to_taxonomy_fp '$id_to_taxonomy_condition.id_to_taxonomy_fp'
            #else if $id_to_taxonomy_condition.source_selector == 'cached'
                --id_to_taxonomy_fp '$id_to_taxonomy_condition.id_to_taxonomy_fp.fields.path'
            #end if
            --assignment_method '$methodcond.assignment_method'
            #if $methodcond.assignment_method == "uclust"
                --min_consensus_fraction '$methodcond.min_consensus_fraction'
                --similarity '$methodcond.similarity'
                --uclust_max_accepts '$methodcond.uclust_max_accepts'
            #else if $methodcond.assignment_method == "rdp"
                #if $methodcond.references.source_selector == 'history'
                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp'
                #else if $methodcond.references.source_selector == 'cached'
                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp.fields.path'
                #end if
                --confidence '$methodcond.confidence'
            #else if $methodcond.assignment_method == "blast"
                #if $methodcond.references.source_selector == 'history'
                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp'
                #else if $methodcond.references.source_selector == 'cached'
                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp.fields.path'
                #end if
                --blast_e_value '$methodcond.blast_e_value'
            #else if $methodcond.assignment_method == "rtax"
                --read_1_seqs_fp '$methodcond.read_1_seqs_fp'
                --read_2_seqs_fp '$methodcond.read_2_seqs_fp'
                $methodcond.single_ok
                $methodcond.no_single_ok_generic
                --read_id_regex '$methodcond.read_id_regex'
                --amplicon_id_regex '$methodcond.amplicon_id_regex'
                --header_id_rege '$methodcond.header_id_regex'
            #else if $methodcond.assignment_method == "mothur"
                #if $methodcond.references.source_selector == 'history'
                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp'
                #else if $methodcond.references.source_selector == 'cached'
                    --reference_seqs_fp '$methodcond.references.reference_seqs_fp.fields.path'
                #end if
                --confidence '$methodcond.confidence'
            #else if $methodcond.assignment_method == "sortmerna"
                --sortmerna_threads \${GALAXY_SLOTS:-1}
                #if $methodcond.sortmerna_db
                    --sortmerna_db '$methodcond.sortmerna_db'

            #end if
            -o assign_taxonomy
    ]]></command>
    <inputs>
        <param argument="--input_fasta_fp" type="data" format="fasta" label="Input fasta file" />

        <conditional name="id_to_taxonomy_condition">
            <param name="source_selector" type="select" label="Do you want to use a taxonomy reference ?">
                <option value="cached">Yes (from the local cache)</option>
                <option value="history">Yes (from the active history)</option>
                <option value="void" selected="true">No</option>
            </param>
            <when value="cached">
                <param argument="--id_to_taxonomy_fp" label="Tab-delimited file mapping sequences to assigned taxonomy" type="select" help="Each assigned taxonomy is provided as a semicolon-separated list. For assignment with rdp, each assigned taxonomy must be exactly 6 levels deep">
                    <options from_data_table="qiime_taxonomy"/>
                </param>
            </when>
            <when value="history">
                <param argument="--id_to_taxonomy_fp" label="Tab-delimited file mapping sequences to assigned taxonomy"  type="data" format="tabular" help="Each assigned taxonomy is provided as a semicolon-separated list. For assignment with rdp, each assigned taxonomy must be exactly 6 levels deep"/>
            </when>
            <when value="void"/>
        </conditional>

        <conditional name="methodcond">
            <param argument="--assignment_method" label="Taxon assignment method" type="select">
                <option selected="True" value="uclust">uclust</option>
                <!--<option value="rdp">rdp</option>-->
                <option value="blast">blast</option>
                <!--<option value="rtax">rtax</option>-->
                <option value="mothur">mothur</option>
                <option value="sortmerna">sortmerna</option>
            </param>
            <when value="uclust">
                <param argument="--min_consensus_fraction" type="float" value="0.51" label="Minimum fraction of database hits that must have a specific taxonomic assignment to assign that taxonomy to a query"/>
                <param argument="--similarity" type="float" value="0.9" label="Minimum percent similarity (expressed as a fraction between 0 and 1) to consider a database match a hit"/>
                <param argument="uclust_max_accepts" type="integer" value="3" label="Number of database hits to consider when making an assignment"/>
            </when>
            <when value="rdp">
                <expand macro="assign_taxonomy_reference_source"/>
                <param argument="--confidence" type="float" value="0.5" label="Minimum confidence to record an assignment"/>
            </when>
            <when value="blast">
                <expand macro="assign_taxonomy_reference_source"/>
                <param argument="--blast_e_value" type="float" value="0.001" label="Maximum e-value to record an assignment"/>
            </when>
            <when value="rtax">
                <param argument="--read_1_seqs_fp" type="data" format="fasta" label="First reads from paired-end sequencing, prior to OTU clustering" help="This file is the result of split_illumina_fastq"/>
                <param argument="--read_2_seqs_fp" type="data" format="fasta" label="Second reads from paired-end sequencing, prior to OTU clustering" help="This file is the result of split_illumina_fastq"/>

                <param argument="--read_id_regex" type="text" value="\S+\s+(\S+)" label="Regex used to parse the result of OTU clustering, to get the read_1_id for each clusterID" help="The clusterID itself is assumed to be the first field, and is not captured by the regex"/>
                <param argument="--amplicon_id_regex" type="text" value="(\S+)\s+(\S+?)\/" label="Regex used to parse the result of split_libraries, to get the ampliconID for each read_1_id" help="Two groups capture read_1_id and ampliconID,  respectively."/>
                <param argument="--header_id_regex" type="text" value="\S+\s+(\S+?)\/" label="Regex used to parse the result of split_libraries, to get the portion of the header that RTAX uses to match mate pairs" help="The default uses the amplicon ID, not including /1 or /3, as the primary key for the query sequences. Typically this regex will be the same as amplicon_id_regex, except that only the second group is captured" />
            </when>
            <when value="mothur">
                <expand macro="assign_taxonomy_reference_source"/>
                <param argument="--confidence" type="float" value="0.5" label="Minimum confidence to record an assignment"/>
            </when>
            <when value="sortmerna">
                <!--<param argument="- -sortmerna_db" type="data" format="fasta" label="Pre-existing database to search against" optional="True"/>-->
                <param argument="--min_consensus_fraction" type="float" value="0.51" label="Minimum fraction of database hits that must have a specific taxonomic assignment to assign that taxonomy to a query"/>
                <param argument="--similarity" type="float" value="0.9" label="Minimum percent similarity (expressed as a fraction between 0 and 1) to consider a database match a hit"/>
                <param argument="--sortmerna_e_value" type="float" value="1.0" label="Maximum E-value when clustering"/>
                <param argument="--sortmerna_coverage" type="float" value="0.9" label="Mininum percent query coverage (of an alignment) to consider a hit, expressed as a fraction between 0 and 1"/>
                <param argument="--sortmerna_best_N_alignments" type="integer" value="5" label="Number best alignments per read to be written"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="log" format="txt" from_work_dir="assign_taxonomy/*_assignments.log" label="${tool.name} on ${on_string}: Log">
            <filter>methodcond['assignment_method']!="mothur"</filter>
        </data>
        <data name="tax_assignments" format="txt" from_work_dir="assign_taxonomy/*.txt" label="${tool.name} on ${on_string}: Taxonomic assignment"/>
        <data name="sortmerna_map" format="tabular" from_work_dir="assign_taxonomy/sortmerna_map.blast" label="${tool.name} on ${on_string}: SortMeRNA Blast">
            <filter>methodcond['assignment_method']=="sortmerna"</filter>
        </data>
    </outputs>
    <tests>
        <!-- Uclust assignment method -->
        <test>
            <param name="input_fasta_fp" value="assign_taxonomy/uclust_input_seqs.fasta"/>
            <conditional name="id_to_taxonomy_condition">
                <param name="source_selector" value="void" />
            </conditional>
            <conditional name="methodcond">
                <param name="assignment_method" value="uclust"/>
                <param name="min_consensus_fraction" value="0.51"/>
                <param name="similarity" value="0.9"/>
                <param name="uclust_max_accepts" value="3" />
            </conditional>
            <output name="tax_assignments" md5="57b0cf51fc0142f369134ea923d78d99"/>
            <output name="log">
                <assert_contents>
                    <has_text text="UclustConsensusTaxonAssigner" />
                    <has_text text="2751331" />
                </assert_contents>
            </output>
        </test>
        <!-- Mothur assignment method -->
        <!-- Note: there is variability in the assignment results with this method so the md5 checksum comparison is not possible -->
        <test>
            <param name="input_fasta_fp" value="assign_taxonomy/mothur_repr_set_seqs.fasta"/>
            <conditional name="id_to_taxonomy_condition">
                <param name="source_selector" value="history" />
                <param name="id_to_taxonomy_fp" value="assign_taxonomy/mothur_id_to_taxonomy.txt"/>
            </conditional>
            <conditional name="methodcond">
                <param name="assignment_method" value="mothur"/>
                <conditional name="references">
                    <param name="source_selector" value="history" />
                    <param name="reference_seqs_fp" value="assign_taxonomy/mothur_ref_seq_set.fna" />
                </conditional>
                <param name="confidence" value="0.5"/>
            </conditional>
            <output name="tax_assignments">
                <assert_contents>
                    <has_text text="X67228" />
                    <has_text text="Rhizobium" />
                    <has_text text="EF503697" />
                </assert_contents>
            </output>
        </test>
        <!-- Blast assignment method -->
        <test>
            <param name="input_fasta_fp" value="assign_taxonomy/mothur_repr_set_seqs.fasta"/>
            <conditional name="id_to_taxonomy_condition">
                <param name="source_selector" value="history" />
                <param name="id_to_taxonomy_fp" value="assign_taxonomy/mothur_id_to_taxonomy.txt"/>
            </conditional>
            <conditional name="methodcond">
                <param name="assignment_method" value="blast"/>
                <conditional name="references">
                    <param name="source_selector" value="history" />
                    <param name="reference_seqs_fp" value="assign_taxonomy/mothur_ref_seq_set.fna" />
                </conditional>
                <param name="blast_e_value" value="0.001"/>
            </conditional>
            <output name="tax_assignments" md5="5ab8d28f67bcbf828937d222b2ab9c6e"/>
            <output name="log">
                <assert_contents>
                    <has_text text="BlastTaxonAssigner" />
                    <has_text text="inspected: 2" />
                </assert_contents>
            </output>
        </test>
        <!-- SortMeRNA assignment method -->
        <!-- Note: The input file has been reduced to only 1 sequence but this test is still quite long to execute (more than 10min) -->
        <!--<test>
            <param name="input_fasta_fp" value="assign_taxonomy/sortmerna_input_seqs.fasta"/>
            <conditional name="methodcond">
                <param name="assignment_method" value="sortmerna"/>
                <param name="min_consensus_fraction" value="0.51" />
                <param name="similarity" value="0.9" />
                <param name="sortmerna_e_value" value="1.0" />
                <param name="sortmerna_coverage" value="0.9" />
                <param name="sortmerna_best_N_alignments" value="5" />
            </conditional>
            <output name="log">
                <assert_contents>
                    <has_text text="Application:SortMeRNA" />
                    <has_text text="min_consensus_fraction" />
                </assert_contents>
            </output>
            <output name="tax_assignments" md5="0da68ab9762b677a00f34051eadad68c"/>
            <output name="sortmerna_map" md5="16e349be29f121fca741d6294f79ce7c"/>
        </test>-->
    </tests>
    <help><![CDATA[
**What it does**