comparison meryl.xml @ 7:51c2360aa807 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/meryl commit 914fb45ccf9c8a5a397dff0efd2b52ecd42823e8"

6:31fa26c0692b

<tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@' profile='20.01'>
    <description>a genomic k-mer counter and sequence utility</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='edam_ontology' />

                <param name="count_operations" type="select" label="Count operations" help="Select an operation to be executed">
                    <option value="count">Count: count the occurrences of canonical k-mers</option>
                    <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option>
                    <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option>
                </param>
                <param name="input_reads" type="data" format="fastq,fasta" label="Input sequences" help="Select your reads in FASTA/FASTQ format." />
                <conditional name="options_kmer_size">
                    <param name="kmer_size" type="select" label="K-mer size selector">
                        <option value="provide">Set a k-mer size</option>
                        <option value="estimate">Estimate the best k-mer size</option>
                    </param>

            </when>
            <when value="print">
                <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" />
            </when>
            <when value="trio-mode">
                <param name="child_reads" type="data" format="fastq,fasta" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" />
                <param name="paternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly" />
                <param name="maternal_reads" type="data" format="fastq,fasta" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly" />
                <conditional name="options_kmer_size">
                    <param name="kmer_size" type="select" label="K-mer size selector">
                        <option value="provide">Set a k-mer size</option>
                        <option value="estimate">Estimate the best k-mer size</option>
                    </param>

                <assert_contents>
                    <has_size value="56100" delta="300" />
                </assert_contents>
            </output>
        </test>
        <!-- test 11 -->
        <test expect_num_outputs="1">
            <conditional name="operation_type">
                <param name="command_type" value="arithmetic-kmers" />
                <param name="arithmetic_operations" value="modulo" />
                <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
                <param name="X" value="3" />
            </conditional>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="37172" delta="300" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="operation_type">

            <conditional name="operation_type">
                <param name="command_type" value="print" />
                <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" />
            </conditional>
            <output name="read_db_print" file="output_25.read-db.tabular" sort="True"/>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark

7:51c2360aa807

<tool id='meryl' name='Meryl' version='@TOOL_VERSION@+@GALAXY_TOOL_VERSION@@SUFFIX_VERSION@' profile='20.01'>
    <description>a genomic k-mer counter and sequence utility</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro='edam_ontology' />

                <param name="count_operations" type="select" label="Count operations" help="Select an operation to be executed">
                    <option value="count">Count: count the occurrences of canonical k-mers</option>
                    <option value="count-forward">Count-forward: count the occurreces of forward k-mers</option>
                    <option value="count-reverse">Count-reverse: count the occurreces of reverse k-mers</option>
                </param>
                <param name="input_reads" type="data" format="fastq,fastq.gz,fasta,fasta.gz" label="Input sequences" help="Select your reads in FASTA/FASTQ format." />
                <conditional name="options_kmer_size">
                    <param name="kmer_size" type="select" label="K-mer size selector">
                        <option value="provide">Set a k-mer size</option>
                        <option value="estimate">Estimate the best k-mer size</option>
                    </param>

            </when>
            <when value="print">
                <param name="input_meryldb_02" type="data" format="meryldb" label="Input meryldb" />
            </when>
            <when value="trio-mode">
                <param name="child_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" label="F1 reads" help="Select F1 reads used for generating the assembly" />
                <param name="paternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Paternal reads" help="Select the paternal reads used for generating the assembly" />
                <param name="maternal_reads" type="data" format="fastq,fasta,fastq.gz,fasta.gz" multiple="true" optional="true" label="Maternal reads" help="Select the maternal reads used for generating the assembly" />
                <conditional name="options_kmer_size">
                    <param name="kmer_size" type="select" label="K-mer size selector">
                        <option value="provide">Set a k-mer size</option>
                        <option value="estimate">Estimate the best k-mer size</option>
                    </param>

                <assert_contents>
                    <has_size value="56100" delta="300" />
                </assert_contents>
            </output>
        </test>
        <!-- test 12 -->
        <test expect_num_outputs="1">
            <conditional name="operation_type">
                <param name="command_type" value="arithmetic-kmers" />
                <param name="arithmetic_operations" value="modulo" />
                <param name="input_meryldb_02" value="read-db.meryldb" ftype="meryldb" />
                <param name="X" value="3" />
            </conditional>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="37501" delta="300" />
                </assert_contents>
            </output>
        </test>
        <test expect_num_outputs="1">
            <conditional name="operation_type">

            <conditional name="operation_type">
                <param name="command_type" value="print" />
                <param name="input_meryldb_02" value="maternal.meryldb" ftype="meryldb" />
            </conditional>
            <output name="read_db_print" file="output_25.read-db.tabular" sort="True"/>
        </test>
        <!--Test compressed files-->
        <test expect_num_outputs="1">
            <conditional name="operation_type">
                <param name="command_type" value="count-kmers" />
                <param name="count_operation" value="count" />
                <param name="input_reads" value="child.fasta.gz" />
                <conditional name="options_kmer_size">
                    <param name="kmer_size" value="provide" />
                    <param name="input_kmer_size" value="7" />
                </conditional>
            </conditional>
            <output name="read_db" ftype="meryldb">
                <assert_contents>
                    <has_size value="1851" delta="300" />
                </assert_contents>
            </output>
            <assert_stdout>
                <has_line line="K-mer size: 7" />
            </assert_stdout>
        </test>
    </tests>
    <help><![CDATA[

.. class:: infomark