comparison megahit_wrapper.xml @ 4:de387b2b2803 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit d44d890566efb82b4ce8a9ed2903b0902f3884ca

3:98242353faa4

<?xml version='1.0' encoding='utf-8'?>
<tool id="megahit" name="MEGAHIT" version="@VERSION@.3">
    <description>for metagenomics assembly</description>
    <macros>
        <token name="@VERSION@">1.1.2</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">megahit</requirement>
    </requirements>
    <version_command>megahit --version</version_command>

            -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.batchmode.pair_input_list]) }
        #else:
            -1 '${input_option.batchmode.pair_input.forward}'
            -2 '${input_option.batchmode.pair_input.reverse}'
        #end if
    #else
        -r '${input_option.single_files}'
    #end if
    ##basic assembly
    --min-count '${basic_section.min_count}'
    --k-min '${basic_section.k_min}'
    --k-max '${basic_section.k_max}'
    --k-step '${basic_section.k_step}'
    --min-contig-len '${basic_section.min_contig_len}'
    ##advanced assembly
    ${advanced_section.nomercy}
    --bubble-level '${advanced_section.bubble_level}'
    --merge-level '${advanced_section.merge_level}'
    --prune-level '${advanced_section.prune_level}'
    --prune-depth '${advanced_section.prune_depth}'
    --low-local-ratio '${advanced_section.low_local_ratio}'
    ${advanced_section.nolocal}
    ${advanced_section.kmin1pass}
&& cat megahit_out/log
    ]]></command>
    <inputs>
        <conditional name="input_option">
            <param name="choice" type="select" label="Select your input option">
                <option value="single" selected="true">Single</option>
                <option value="paired">Paired-end</option>
                <option value="paired_collection">Paired-end collection</option>
            </param>
            <when value="single">
                <param name="single_files" argument="-r" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Single-end file(s)" help="FASTQ/FASTA/FASTQ.GZ files accepted" />
            </when>
            <when value="paired">
                <param name="fastq_input1" argument="-1" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 1 input reads"/>
                <param name="fastq_input2" argument="-2" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 2 input reads"/>
            </when>

                </when>
              </conditional>
            </when>
        </conditional>
        <section name="basic_section" title="Basic assembly options" expanded="True">
            <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />
            <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers"/>
            <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size" max="255" help="must be odd number"/>
            <param name="k_max" argument="--k-max" type="integer" value="141" label="maximum kmer size" max="255" help="must be odd number"/>
            <param name="k_step" argument="--k-step" type="integer" value="12" label="increment of kmer size of each iteration" max="28" help="must be even number"/>
        </section>
        <section name="advanced_section" title="Advanced assembly options" expanded="False">
            <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue=""  label="do not add mercy kmers" />
            <param name="bubble_level" argument="--bubble-level" type="integer" value="2" min="0" max="2" label="intensity of bubble merging (0-2), 0 to disable" />
            <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles of length " value="20,0.95" />
            <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="strength of low depth pruning" />
            <param name="prune_depth" argument="--prune-depth" type="integer" value="2" min="0" label="remove unitigs with avg kmer depth less than this value" />
            <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="ratio threshold to define low local coverage contigs" />
            <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" />
            <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="use 1pass mode to build SdBG of k_min" />
        </section>
    </inputs>
    <outputs>
        <data format="fasta" name="output" from_work_dir="megahit_out/final.contigs.fa" label="Assembly with ${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <conditional name="input_option">
                <param name="choice" value="single"/>

              <has_line_matching expression=">k21_1 flag=3 multi=1.0486 len=576" />
            </assert_contents>
            </output>
        </test>
        <test>
            <conditional name="input_option">
                <param name="choice" value="paired"/>
                <param name="fastq_input1" value="paired-fq1.fa"/>
                <param name="fastq_input2" value="paired-fq2.fa"/>
            </conditional>
            <output name="output" file="paired_result.fa"/>
        </test>
        <test>
          <conditional name="input_option">
            <param name="choice" value="paired_collection"/>
            <conditional name="batchmode">
              <param name="processmode" value="merge"/>
              <param name="pair_input_list">
                <collection type="list:paired">
                <element name="Pair1">
                  <collection type="paired">
                    <element name="forward" value="paired-fq1.fa" ftype="fasta"/>
                    <element name="reverse" value="paired-fq2.fa" ftype="fasta"/>
                  </collection>
                </element>
                </collection>
              </param>
            </conditional>
          </conditional>
          <output name="output" file="paired_result.fa"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**

4:de387b2b2803

<?xml version='1.0' encoding='utf-8'?>
<tool id="megahit" name="MEGAHIT" version="@VERSION@.4">
    <description>for metagenomics assembly</description>
    <macros>
        <token name="@VERSION@">1.1.3</token>
    </macros>
    <requirements>
        <requirement type="package" version="@VERSION@">megahit</requirement>
    </requirements>
    <version_command>megahit --version</version_command>

            -2 ${ ','.join(['"%s"' % x.reverse for x in $input_option.batchmode.pair_input_list]) }
        #else:
            -1 '${input_option.batchmode.pair_input.forward}'
            -2 '${input_option.batchmode.pair_input.reverse}'
        #end if
    #else if $input_option.choice == 'interleaved'
        --12 '${input_option.interleaved_file}'
    #else
        -r '${input_option.single_files}'
    #end if
    ##basic assembly
    --min-count '${basic_section.min_count}'
    #if $basic_section.k_mer.k_mer_method == "klist_method":
        --k-list '${basic_section.k_mer.k_list}'
    #else:
        --k-step '${basic_section.k_mer.k_step}'
        --k-min '${basic_section.k_mer.k_min}'
        --k-max '${basic_section.k_mer.k_max}'
    #end if
    ##advanced assembly
    ${advanced_section.nomercy}
    --bubble-level '${advanced_section.bubble_level}'
    --merge-level '${advanced_section.merge_level}'
    --prune-level '${advanced_section.prune_level}'
    --prune-depth '${advanced_section.prune_depth}'
    --low-local-ratio '${advanced_section.low_local_ratio}'
    ${advanced_section.nolocal}
    ${advanced_section.kmin1pass}
    --min-contig-len '${output_section.min_contig_len}'
&& cat megahit_out/log
    ]]></command>
    <inputs>
        <conditional name="input_option">
            <param name="choice" type="select" label="Select your input option">
                <option value="single" selected="true">Single</option>
                <option value="interleaved">Interleaved-paired-end</option>
                <option value="paired">Paired-end</option>
                <option value="paired_collection">Paired-end collection</option>
            </param>
            <when value="single">
                <param name="single_files" argument="-r" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz,fastq.bz2" multiple="true" label="Single-end file(s)" help="Accepts fasta (.fasta, .fa) and fastq (.fastq) formats as well as gzip (.gz) and gzip2 (.bz2) files" />
            </when>
            <when value="interleaved">
                <param name="interleaved_file" argument="--12" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz,fastq.bz2" multiple="true" label="Interleaved-paired-end file(s)" help="Accepts fasta (.fasta, .fa) and fastq (.fastq) formats as well as gzip (.gz) and gzip2 (.bz2) files" />
            </when>
            <when value="paired">
                <param name="fastq_input1" argument="-1" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 1 input reads"/>
                <param name="fastq_input2" argument="-2" type="data" format="fastq,fastqsanger,fasta,fastq.gz,fastqsanger.gz" multiple="true" label="Mate 2 input reads"/>
            </when>

                </when>
              </conditional>
            </when>
        </conditional>
        <section name="basic_section" title="Basic assembly options" expanded="True">
            <param name="min_count" argument="--min-count" type="integer" value="2" label="minimum multiplicity for filtering (k_min+1)-mers" help="(kmin+1)-mer with multiplicity lower than d (default 2, specified by --min-count option) will be discarded. You should be cautious to set d less than 2, which will lead to a much larger and noisy graph. We recommend using the default value 2 for metagenomics assembly. If you want to use MEGAHIT to do generic assemblies, please change this value according to the sequencing depth. (recommend --min-count 3 for >40x)."/>
            <conditional name="k_mer">
                <param name="k_mer_method" type="select" label="K-mer specification method">
                    <option value="klist_method">Specify list</option>
                    <option value="klim_method">Specify min, max, and step values</option>
                </param>
                <when value="klist_method">
                    <param name="k_list" argument="--k-list" type="text" value="21,29,39,59,79,99,119,141" label="comma-separated list of kmer size" help="all must be odd, in the range 15-255, and with increments &lt;= 28"/>
                </when>
                <when value="klim_method"> 
                    <param name="k_min" argument="--k-min" type="integer" value="21" label="minimum kmer size." max="255" help="Must be odd number. For ultra complex metagenomics data such as soil, a larger kmin, say 27, is recommended to reduce the complexity of the de Bruijn graph. Quality trimming is also recommended. For high-depth generic data, large --k-min (25 to 31) is recommended. Smaller --k-step, say 10, is more friendly to low-coverage datasets."/>
                    <param name="k_max" argument="--k-max" type="integer" value="141" label="maximum kmer size" max="255" help="must be odd number"/>
                    <param name="k_step" argument="--k-step" type="integer" value="12" label="increment of kmer size of each iteration" max="28" help="must be even number"/>
                </when>
            </conditional>
        </section>
        <section name="advanced_section" title="Advanced assembly options" expanded="False">
            <param name="nomercy" type="boolean" checked="false" truevalue="--no-mercy" falsevalue=""  label="do not add mercy kmers" help="Mercy kmers are specially designed for metagenomics assembly to recover low coverage sequences. For generic dataset >= 30x, MEGAHIT may generate better results with no mercy kmers." />
            <param name="bubble_level" argument="--bubble-level" type="integer" value="2" min="0" max="2" label="intensity of bubble merging (0-2), 0 to disable" />
            <param name="merge_level" argument="--merge-level" type="text" label="merge complex bubbles of length " value="20,0.95" />
            <param name="prune_level" argument="--prune-level" type="integer" value="2" min="0" max="3" label="strength of low depth pruning" />
            <param name="prune_depth" argument="--prune-depth" type="integer" value="2" min="0" label="remove unitigs with avg kmer depth less than this value" />
            <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="ratio threshold to define low local coverage contigs" />
            <param name="nolocal" type="boolean" checked="false" truevalue="--no-local" falsevalue="" label="disable local assembly" />
            <param name="kmin1pass" type="boolean" checked="false" truevalue="--kmin-1pass" falsevalue="" label="use 1pass mode to build SdBG of k_min" />
        </section>
        <section name="output_section" title="Output options" expanded="True">
            <param name="min_contig_len" argument="--min-contig-len" type="integer" value="200" label="minimum length of contigs to output" />
            <param name="show_intermediate_contigs" type="boolean" checked="false" label="Return intermediate contigs?"/>
        </section>
    </inputs>
    <outputs>
        <data format="fasta" name="output" from_work_dir="megahit_out/final.contigs.fa" label="Assembly with ${tool.name} on ${on_string}" />
        <collection name="intermediate_contigs" type="list" label="Intermediate contigs from ${tool.name} on ${on_string}">
            <filter>output_section['show_intermediate_contigs']</filter>
            <discover_datasets pattern="(?P&lt;designation&gt;.*\d)\.contigs\.fa$" ext="fasta" directory="megahit_out/intermediate_contigs" />
        </collection>
    </outputs>
    <tests>
        <test>
            <conditional name="input_option">
                <param name="choice" value="single"/>

              <has_line_matching expression=">k21_1 flag=3 multi=1.0486 len=576" />
            </assert_contents>
            </output>
        </test>
        <test>
             <conditional name="input_option">
                <param name="choice" value="interleaved"/>
                <param name="interleaved_file" value="interleaved-fq.fa"/>
            </conditional>
            <output name="output" file="interleaved_result.fa"/>
        </test>
        <test>
            <conditional name="input_option">
                <param name="choice" value="paired"/>
                <param name="fastq_input1" value="paired-fq1.fa"/>
                <param name="fastq_input2" value="paired-fq2.fa"/>
            </conditional>
            <output name="output" file="paired_result.fa"/>
        </test>
        <test>
            <conditional name="input_option">
                <param name="choice" value="paired_collection"/>
                <conditional name="batchmode">
                    <param name="processmode" value="merge"/>
                    <param name="pair_input_list">
                        <collection type="list:paired">
                        <element name="Pair1">
                          <collection type="paired">
                            <element name="forward" value="paired-fq1.fa" ftype="fasta"/>
                            <element name="reverse" value="paired-fq2.fa" ftype="fasta"/>
                          </collection>
                        </element>
                        </collection>
                    </param>
                </conditional>
            </conditional>
            <output name="output" file="paired_result.fa"/>
        </test>
    </tests>
    <help><![CDATA[

**What it does**