comparison megahit_wrapper.xml @ 7:a96f3ad4e0d8 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit 64421702fce231e2fb05bd2f585679154c3e2140

6:14ddfc8ffb93

<?xml version='1.0' encoding='utf-8'?>
<tool id="megahit" name="MEGAHIT" version="@TOOL_VERSION@+galaxy0">
    <description>for metagenomics assembly</description>
    <xrefs>
        <xref type="bio.tools">megahit</xref>
    </xrefs>
    <macros>
        <token name="@TOOL_VERSION@">1.2.9</token>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">megahit</requirement>
    </requirements>
    <version_command>megahit --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
megahit
    --num-cpu-threads \${GALAXY_SLOTS:-4}
    #if $input_option.choice == 'paired'
        -1 '${input_option.fastq_input1}'
        -2 '${input_option.fastq_input2}'

    --low-local-ratio '${advanced_section.low_local_ratio}'
	--cleaning-rounds '${advanced_section.cleaning_rounds}'					  
    ${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">

                </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" value="20,0.95" label="Merge complex bubbles of length" />
            <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="disconnect_ratio" argument="--disconnect-ratio" type="float" value="0.1" label="Disconnect unitigs if its depth is less than this ratio times the total depth of itself and its siblings" />
            <param name="low_local_ratio" argument="--low-local-ratio" type="float" value="0.2" label="Remove unitigs if its depth is less than this ratio times the average depth of the neighborhoods" />
			<param name="cleaning_rounds" argument="--cleaning-rounds" type="integer" value="5" label="Number of rounds for graph cleanning" />	  
            <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}" />

            <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"/>
                <param name="single_files" value="refExample.fa" ftype="fasta"/>
            </conditional>
            <output name="output">
            <assert_contents>
              <has_line_matching expression=">k21_0 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">

7:a96f3ad4e0d8

<tool id="megahit" name="MEGAHIT" version="@TOOL_VERSION@+galaxy1">
    <description>for metagenomics assembly</description>
    <macros>
        <token name="@TOOL_VERSION@">1.2.9</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">megahit</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">megahit</requirement>
    </requirements>
    <version_command>megahit --version</version_command>
    <command detect_errors="exit_code"><![CDATA[
if [[ -n "\$GALAXY_MEMORY_MB" ]]; then
    MEMORY="-m \$((GALAXY_MEMORY_MB * 1024))";
fi;

megahit
    --num-cpu-threads \${GALAXY_SLOTS:-4}
    #if $input_option.choice == 'paired'
        -1 '${input_option.fastq_input1}'
        -2 '${input_option.fastq_input2}'

    --low-local-ratio '${advanced_section.low_local_ratio}'
	--cleaning-rounds '${advanced_section.cleaning_rounds}'					  
    ${advanced_section.nolocal}
    ${advanced_section.kmin1pass}
    --min-contig-len '${output_section.min_contig_len}'
    \$MEMORY
&& cat megahit_out/log
    ]]></command>
    <inputs>
        <conditional name="input_option">
            <param name="choice" type="select" label="Select your input option">

                </when>
              </conditional>
            </when>
        </conditional>
        <section name="basic_section" title="Basic assembly options" expanded="True">
            <param 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 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 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 argument="--k-max" type="integer" value="141" label="Maximum kmer size" max="255" help="must be odd number"/>
                    <param 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 argument="--bubble-level" type="integer" value="2" min="0" max="2" label="Intensity of bubble merging (0-2), 0 to disable" />
            <param argument="--merge-level" type="text" value="20,0.95" label="Merge complex bubbles of length" />
            <param argument="--prune-level" type="integer" value="2" min="0" max="3" label="Strength of low depth pruning" />
            <param argument="--prune-depth" type="integer" value="2" min="0" label="Remove unitigs with avg kmer depth less than this value" />
			<param argument="--disconnect-ratio" type="float" value="0.1" label="Disconnect unitigs if its depth is less than this ratio times the total depth of itself and its siblings" />
            <param argument="--low-local-ratio" type="float" value="0.2" label="Remove unitigs if its depth is less than this ratio times the average depth of the neighborhoods" />
			<param argument="--cleaning-rounds" type="integer" value="5" label="Number of rounds for graph cleanning" />	  
            <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 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}" />

            <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 expect_num_outputs="1">
            <conditional name="input_option">
                <param name="choice" value="single"/>
                <param name="single_files" value="refExample.fa" ftype="fasta"/>
            </conditional>
            <output name="output">
            <assert_contents>
              <has_line_matching expression=">k21_0 flag=3 multi=1.0486 len=576" />
            </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
             <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 expect_num_outputs="1">
            <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 expect_num_outputs="1">
            <conditional name="input_option">
                <param name="choice" value="paired_collection"/>
                <conditional name="batchmode">
                    <param name="processmode" value="merge"/>
                    <param name="pair_input_list">