comparison megahit_wrapper.xml @ 8:ab208c87d973 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/megahit commit acac4f9e3f82cc7248177b97d1cbabbf58d24cf6

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>

	--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">
                <option value="single" selected="true">Single</option>

            <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}" />
        <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 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"/>

8:ab208c87d973

<tool id="megahit" name="MEGAHIT" version="@TOOL_VERSION@+galaxy2">
    <description>for metagenomics assembly</description>
    <macros>
        <token name="@TOOL_VERSION@">1.2.9</token>
    </macros>
    <xrefs>

	--cleaning-rounds '${advanced_section.cleaning_rounds}'					  
    ${advanced_section.nolocal}
    ${advanced_section.kmin1pass}
    --min-contig-len '${output_section.min_contig_len}'
    \$MEMORY
    ]]></command>
    <inputs>
        <conditional name="input_option">
            <param name="choice" type="select" label="Select your input option">
                <option value="single" selected="true">Single</option>

            <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?"/>
            <param name="log_file" type="boolean" label="Generate a log file" help="Generates a log file, which can be used as MultiQC input"/>
        </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>
        <data name="log_output" format="txt" label="${tool.name} on ${on_string} (Log file)" from_work_dir="megahit_out/log">
            <filter>output_section['log_file']</filter>
        </data>
    </outputs>
    <tests>
        <test expect_num_outputs="2">
            <conditional name="input_option">
                <param name="choice" value="single"/>
                <param name="single_files" value="refExample.fa" ftype="fasta"/>
            </conditional>
            <param name="log_file" value="true"/>
            <output name="output">
            <assert_contents>
              <has_line_matching expression=">k21_0 flag=3 multi=1.0505 len=576" />
            </assert_contents>
            </output>
            <output name="log_output">
                <assert_contents>
                    <has_text text="- MEGAHIT v"/>
                    <has_text text="- Build graph for k = 21"/>
                    <has_text text="- Assemble contigs from SdBG for k = 21"/>
                    <has_text text="- Local assembly for k = 21"/>
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
             <conditional name="input_option">
                <param name="choice" value="interleaved"/>