comparison quast.xml @ 12:875d0f36d66f draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/quast commit f713a7853d074ca39057c680ebadba5cbecf5d86"

11:7594365c546b

                <option value="nanopore">Nanopore reads</option>
            </param>
            <when value="disabled"/>

            <when value="single">
                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" />
            </when>

            <when value="paired">
                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #1" />
                <param name="input_2" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #2" />
            </when>

            <when value="paired_interlaced">
                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" />
            </when>

            <when value="mate_paired">
                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #1" />
                <param name="input_2" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file #2" />
            </when>

            <when value="pacbio">
                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" />
            </when>

            <when value="nanopore">
                <param name="input_1" format="fastq,fastq.gz" type="data" multiple="true" label="FASTQ file" />
            </when>
        </conditional>

        <conditional name="assembly">
            <param name="type" type="select" label="Type of assembly">

                <param name="skip_unaligned_mis_contigs" value="true"/>
                <param name="fragmented_max_indent" value="50"/>
            </section>
            <param name="output_files" value="html"/>
            <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/>
            <output name="circos_output" file="test1_circos.png" ftype="png"/>
        </test>
        <!-- Test 02: all outputs -->
        <test expect_num_outputs="8">
            <conditional name="in">
                <param name="custom" value="true"/>

                <param name="reads_option" value="single"/>
                <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
            </conditional>
            <param name="output_files" value="tabular"/>
            <output name="quast_tabular" file="test6.tab" ftype="tabular"/>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

12:875d0f36d66f

                <option value="nanopore">Nanopore reads</option>
            </param>
            <when value="disabled"/>

            <when value="single">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>

            <when value="paired">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
                <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
            </when>

            <when value="paired_interlaced">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>

            <when value="mate_paired">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #1" />
                <param name="input_2" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file #2" />
            </when>

            <when value="pacbio">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>

            <when value="nanopore">
                <param name="input_1" format="fastq,fastq.gz,fasta,fasta.gz" type="data" multiple="true" label="FASTQ/FASTA file" />
            </when>
        </conditional>

        <conditional name="assembly">
            <param name="type" type="select" label="Type of assembly">

                <param name="skip_unaligned_mis_contigs" value="true"/>
                <param name="fragmented_max_indent" value="50"/>
            </section>
            <param name="output_files" value="html"/>
            <output name="report_html" file="test1_report.html" ftype="html" compare="sim_size"/>
            <output name="circos_output" file="test1_circos.png" ftype="png" compare="sim_size"/>
        </test>
        <!-- Test 02: all outputs -->
        <test expect_num_outputs="8">
            <conditional name="in">
                <param name="custom" value="true"/>

                <param name="reads_option" value="single"/>
                <param name="input_1" value="pacbio_01.fastq.gz,pacbio_02.fastq.gz"/>
            </conditional>
            <param name="output_files" value="tabular"/>
            <output name="quast_tabular" file="test6.tab" ftype="tabular"/>
        </test>
        <!-- Test 7: FASTA.gz read files -->
        <test expect_num_outputs="1">
            <conditional name="in">
                <param name="custom" value="true"/>
                <repeat name="inputs">
                    <param name="input" value="contigs1.fna"/>
                    <param name="labels" value="contig1"/>
                </repeat>
                <repeat name="inputs">
                    <param name="input" value="contigs2.fna"/>
                    <param name="labels" value="contig2"/>
                </repeat>
            </conditional>
            <conditional name="reads">
                <param name="reads_option" value="single"/>
                <param name="input_1" value="pacbio_01.fasta.gz,pacbio_02.fasta.gz"/>
            </conditional>
            <param name="output_files" value="tabular"/>
            <output name="quast_tabular" file="test7.tab" ftype="tabular"/>
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**