annotate das_tool.xml @ 5:b048a987dd7d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/das_tool commit b50985039ff11e1779f9f48f13e3b74fa1c0e955

<tool id="das_tool" name="DAS Tool" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>for genome-resolved metagenomics</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="version"/>
    <command detect_errors="exit_code"><![CDATA[
#import re

#set $bins = []
#set $labels = []
#for $i, $s in enumerate($binning)
    #silent $bins.append(str($s.bins))
    #if $s.labels != ''
        #silent $labels.append(str($s.labels))
    #else
        #silent $labels.append(re.sub('[^\w\-_\.]', '_', $s.bins.element_identifier))
    #end if
#end for

#if $adv.proteins
    ln -s '$adv.proteins' 'proteins' &&
#end if

#set $bins = ','.join($bins)
#set $labels = ','.join($labels)

DAS_Tool
    --contigs '$contigs'
    --outputbasename 'outputs'
    --bins '$bins'
    --labels '$labels'
    --search_engine '$adv.search_engine'
    #if $adv.proteins
        --proteins 'proteins'
    #end if
    --score_threshold $adv.score_threshold
    --duplicate_penalty $adv.duplicate_penalty
    --megabin_penalty $adv.megabin_penalty
    --max_iter_post_threshold $adv.max_iter_post_threshold

    $output.write_bin_evals
    $output.write_bins.write_bins
    #if str($output.write_bins.write_bins) != ''
        $output.write_bins.write_unbinned
    #end if
    $output.debug
    --threads \${GALAXY_SLOTS:-1}
    ]]></command>
    <inputs>
        <param argument="--contigs" type="data" format="fasta" label="Contig sequences"/>
        <repeat name="binning" title="Bins" min="1">
            <param argument="--bins" type="data" format="tabular" label="Contigs-to-bin table" help="Tabular with two columns: contig-IDs and bin-IDs. Fasta_to_Contigs2Bin can be used to  Converts genome bins in fasta format to Contigs-to-bin table"/>
            <param argument="--labels" type="text" value="" label="Name of binning prediction name" help="If left empty the identifier of the contig-to-bin table is used. Only alphanumeric characters, dash, underscore and dor are allowed. Other characters are replaced by underscore.">
                <sanitizer invalid_char="_">
                    <valid initial="string.ascii_letters,string.digits">
                        <add value="-" />
                        <add value="_" />
                        <add value="." />
                    </valid>
                </sanitizer>
            </param>
        </repeat>
        <section name="adv" title="Advanced options">
            <param argument="--search_engine" type="select" label="Engine used for single copy gene identification">
                <option value="diamond" selected="true">diamond</option>
                <option value="blastp">blastp</option>
            </param>
            <param argument="--proteins" type="data" format="fasta" optional="true" label="Predicted proteins" help="The file should be prodigal fasta format: >contigID_geneNo"/>
            <param argument="--score_threshold" type="float" min="0" max="1" value="0.5" label="Score threshold until selection algorithm will keep selecting bins"/>
            <param argument="--duplicate_penalty" type="float" min="0" max="3" value="0.6" label="Penalty for duplicate single copy genes per bin (weight b)" help="Only change if you know what you are doing"/>
            <param argument="--megabin_penalty" type="float" min="0" max="3" value="0.5" label="Penalty for megabins (weight c)" help="Only change if you know what you are doing"/>
            <param argument="--max_iter_post_threshold" type="integer" min="1" value="10" label="Maximum number of iterations after reaching score threshold"/>
        </section>
        <section name="output" title="Outputs">
            <param name="proteins" type="boolean" checked="false" label="Output predicted proteins?"/>
            <param argument="--write_bin_evals" type="boolean" truevalue="--write_bin_evals" falsevalue="" checked="false" label="Write evaluation of input bin sets?"/>
            <conditional name="write_bins">
                <param argument="--write_bins" type="select" label="Export bins as fasta files?">
                    <option value="--write_bins" selected="true">Yes</option>
                    <option value="">No</option>
                </param>
                <when value="--write_bins">
                    <param argument="--write_unbinned" type="boolean" truevalue="--write_unbinned" falsevalue="" checked="false" label="Export unbinned contigs as fasta file?"/>
                </when>
                <when value=""/>
            </conditional>
            <param argument="--debug" type="boolean" truevalue="--debug" falsevalue="" checked="false" label="Write debug information to log file?"/>
        </section>
    </inputs>
    <outputs>
        <data name="summary" format="tabular" from_work_dir="outputs_DASTool_summary.tsv" label="${tool.name} on ${on_string}: Summary of output bins" />
        <data name="contigs2bin" format="tabular" from_work_dir="outputs_DASTool_contig2bin.tsv" label="${tool.name} on ${on_string}: Contigs to bin file for the output bins" />
        <data name="log" format="txt" from_work_dir="outputs_DASTool.log" label="${tool.name} on ${on_string}: Log" />
        <data name="eval" format="tabular" from_work_dir="outputs_allBins.eval" label="${tool.name} on ${on_string}: Quality and completeness estimates of input bin sets" >
            <filter>output['write_bin_evals']</filter>
        </data>
        <collection name="bins" type="list" label="${tool.name} on ${on_string}: Bins">
            <filter>output['write_bins']['write_bins'] != ""</filter>
            <discover_datasets pattern="^(?!unbinned\.fa)((?P&lt;designation&gt;.*)\.fa)" format="fasta" directory="outputs_DASTool_bins"/>
          </collection>
        <data name="unbinned_contigs" format="fasta" from_work_dir="outputs_DASTool_bins/unbinned.fa" label="${tool.name} on ${on_string}: Unbinned contigs">
            <filter>output['write_bins']['write_bins'] != "" and output['write_bins']['write_unbinned']</filter>
        </data>
        <data name="proteins" format="fasta" from_work_dir="outputs_proteins.faa" label="${tool.name} on ${on_string}: Proteins" >
            <filter>output['proteins']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="4">
            <param name="contigs" value="contigs.fasta"/>
            <repeat name="binning">
                <param name="bins" value="metabat.tabular"/>
                <param name="labels" value="metabat"/>
            </repeat>
            <section name="adv">
                <param name="search_engine" value="diamond"/>
                <param name="proteins" value="proteins.fasta"/>
                <param name="score_threshold" value="0.5"/>
                <param name="duplicate_penalty" value="0.6"/>
                <param name="megabin_penalty" value="0.5" />
            </section>
            <section name="output">
                <param name="write_bin_evals" value="true"/>
                <conditional name="write_bins">
                    <param name="write_bins" value=""/>
                </conditional>
                <param name="debug" value="true"/>
            </section>
            <output name="summary" ftype="tabular">
                <assert_contents>
                    <has_text text="unique_SCGs"/>
                    <has_text text="metabat.8"/>
                    <has_text text="bacteria"/>
                </assert_contents>
            </output>
            <output name="contigs2bin" ftype="tabular">
                <assert_contents>
                    <has_text text="Ley3_66761_scaffold_6"/>
                </assert_contents>
            </output>
            <output name="log" ftype="txt">
                <assert_contents>
                    <has_text text="Skipping gene prediction"/>
                    <has_text text="#Target sequences to report alignments for: 1"/>
                </assert_contents>
            </output>
            <output name="eval" ftype="tabular">
                <assert_contents>
                    <has_text text="unique_SCGs"/>
                    <has_text text="metabat.8"/>
                </assert_contents>
            </output>
        </test>
        <!-- like the first test, but with empty label  -->
        <test expect_num_outputs="4">
            <param name="contigs" value="contigs.fasta"/>
            <repeat name="binning">
                <param name="bins" value="metabat.tabular"/>
                <!-- <param name="labels" value="metabat"/> -->
            </repeat>
            <section name="adv">
                <param name="search_engine" value="diamond"/>
                <param name="proteins" value="proteins.fasta"/>
                <param name="score_threshold" value="0.5"/>
                <param name="duplicate_penalty" value="0.6"/>
                <param name="megabin_penalty" value="0.5" />
            </section>
            <section name="output">
                <param name="write_bin_evals" value="true"/>
                <conditional name="write_bins">
                    <param name="write_bins" value=""/>
                </conditional>
                <param name="debug" value="true"/>
            </section>
            <output name="summary" ftype="tabular">
                <assert_contents>
                    <has_text text="unique_SCGs"/>
                    <has_text text="metabat.8"/>
                    <has_text text="bacteria"/>
                </assert_contents>
            </output>
            <output name="contigs2bin" ftype="tabular">
                <assert_contents>
                    <has_text text="Ley3_66761_scaffold_6"/>
                </assert_contents>
            </output>
            <output name="log" ftype="txt">
                <assert_contents>
                    <has_text text="Skipping gene prediction"/>
                    <has_text text="#Target sequences to report alignments for: 1"/>
                </assert_contents>
            </output>
            <output name="eval" ftype="tabular">
                <assert_contents>
                    <has_text text="unique_SCGs"/>
                    <has_text text="metabat.8"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="6">
            <param name="contigs" value="contigs.fasta"/>
            <repeat name="binning">
                <param name="bins" value="metabat.tabular"/>
                <param name="labels" value="metabat"/>
            </repeat>
            <section name="adv">
                <param name="search_engine" value="diamond"/>
                <param name="score_threshold" value="0.5"/>
                <param name="duplicate_penalty" value="0.6"/>
                <param name="megabin_penalty" value="0.5" />
            </section>
            <section name="output">
                <param name="proteins" value="true"/>
                <param name="write_bin_evals" value="false"/>
                <conditional name="write_bins">
                    <param name="write_bins" value="--write_bins"/>
                    <param name="write_unbinned" value="true"/>
                </conditional>
                <param name="debug" value="true"/>
            </section>
            <output name="summary" ftype="tabular">
                <assert_contents>
                    <has_text text="unique_SCGs"/>
                    <has_text text="metabat.8"/>
                    <has_text text="bacteria"/>
                </assert_contents>
            </output>
            <output name="contigs2bin" ftype="tabular">
                <assert_contents>
                    <has_text text="Ley3_66761_scaffold_6"/>
                </assert_contents>
            </output>
            <output name="log" ftype="txt">
                <assert_contents>
                    <has_text text="Parameters"/>
                    <has_text text="Predicting genes"/>
                </assert_contents>
            </output>
            <output_collection name="bins" count="1"> <!--unbinned.fa must not appear in bins collection. unbinned.fa appears as additional output below.-->
                <element name="metabat.8" ftype="fasta">
                    <assert_contents>
                        <has_text text=">Ley3_66761_scaffold_6"/>
                    </assert_contents>
                </element>
            </output_collection>
            <output name="unbinned_contigs" ftype="fasta">
                <assert_contents>
                    <has_text text=">Ley3_66761_scaffold_505"/>
                </assert_contents>
            </output>
            <output name="proteins" ftype="fasta">
                <assert_contents>
                    <has_text text="Ley3_66761_scaffold_6_1 # 1 # 786 # 1 #"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
@HELP_HEADER@

Inputs
======

- Bins: Tab-separated files of contig-IDs and bin-IDs. Contigs to bin file example: ::

    Contig_1	bin.01
    Contig_8	bin.01
    Contig_42	bin.02
    Contig_49	bin.03

- Contigs: Assembled contigs in fasta format: ::

    >Contig_1
    ATCATCGTCCGCATCGACGAATTCGGCGAACGAGTACCCCTGACCATCTCCGATTA...
    >Contig_2
    GATCGTCACGCAGGCTATCGGAGCCTCGACCCGCAAGCTCTGCGCCTTGGAGCAGG...

- [Optional] Proteins: Predicted proteins in prodigal fasta format. The header contains contig-ID and gene number: ::

    >Contig_1_1
    MPRKNKKLPRHLLVIRTSAMGDVAMLPHALRALKEAYPEVKVTVATKSLFHPFFEG...
    >Contig_1_2
    MANKIPRVPVREQDPKVRATNFEEVCYGYNVEEATLEASRCLNCKNPRCVAACPVN...

Outputs
=======

- Summary of output bins including quality and completeness estimates
- Contigs to bin file of output bins
- [Optional] Quality and completeness estimates of input bin sets
- [Optional] Bins in fasta format
- [Optional] Unbinned contigs

    ]]></help>
    <expand macro="citations"/>
</tool>