comparison kraken.xml @ 10:766d5f63b0f4 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tool_collections/kraken/ commit 3a94fbf6a188ea81441ef2f654ba5a74bff56f22

9:aec58624706f

        assign taxonomic labels to sequencing reads
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code">
        <![CDATA[
        @SET_DATABASE_PATH@ &&

                <option value="yes">Paired</option>
                <option selected="True" value="no">Single</option>
            </param>
            <when value="collection">
                <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
                <param name="check_names" argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/>
            </when>
            <when value="yes">
                <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
                <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
                <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />

                   help="Quick mode: rather than searching all k-mers in a sequence, stop classification after a specified number of database hit">
                <option value="yes">Yes</option>
                <option selected="True" value="no">No</option>
            </param>
            <when value="yes">
                <param name="min_hits" argument="--min-hits" type="integer" value="1" label="Number of hits required for classification"
                       help="min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/>
            </when>
            <when value="no"/><!-- Do absolutely nothing -->
        </conditional>

        <param name="only_classified_output" argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue=""
               label="Print no Kraken output for unclassified sequences"/>

        <expand macro="input_database" />
    </inputs>
    <outputs>

        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
        <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
    </outputs>

    <tests>
        <test>
            <param name="single_paired_selector" value="no"/>
            <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/>
            <param name="split_reads" value="false"/>
            <param name="quick" value="no"/>
            <param name="only-classified-output" value="false"/>
            <param name="kraken_database" value="old_style_test_entry"/>
            <output name="output" file="kraken/kraken_test1_output.tab" ftype="tabular"/>
        </test>
        <test>
            <param name="single_paired_selector" value="no"/>
            <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/>
            <param name="split_reads" value="false"/>
            <param name="quick" value="no"/>
            <param name="only-classified-output" value="false"/>

10:766d5f63b0f4

        assign taxonomic labels to sequencing reads
    </description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="exit_code">
        <![CDATA[
        @SET_DATABASE_PATH@ &&

                <option value="yes">Paired</option>
                <option selected="True" value="no">Single</option>
            </param>
            <when value="collection">
                <param format="fasta,fastq" name="input_pair" type="data_collection" collection_type="paired" label="Collection of paired reads" help="FASTA or FASTQ datasets" />
                <param argument="--check-names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match"/>
            </when>
            <when value="yes">
                <param format="fasta,fastq" name="forward_input" type="data" label="Forward strand" help="FASTA or FASTQ dataset"/>
                <param format="fasta,fastq" name="reverse_input" type="data" label="Reverse strand" help="FASTA or FASTQ dataset"/>
                <param name="check_names" type="boolean" checked="False" truevalue="--paired --check-names" falsevalue="--paired" label="Verify read names match" help="--check-names" />

                   help="Quick mode: rather than searching all k-mers in a sequence, stop classification after a specified number of database hit">
                <option value="yes">Yes</option>
                <option selected="True" value="no">No</option>
            </param>
            <when value="yes">
                <param argument="--min-hits" type="integer" value="1" label="Number of hits required for classification"
                       help="min-hits will allow you to require multiple hits before declaring a sequence classified, which can be especially useful with custom databases when testing to see if sequences either do or do not belong to a particular genome; default=1"/>
            </when>
            <when value="no"/><!-- Do absolutely nothing -->
        </conditional>

        <param argument="--only-classified-output" type="boolean" checked="False" truevalue="--only-classified-output" falsevalue=""
               label="Print no Kraken output for unclassified sequences"/>

        <expand macro="input_database" />
    </inputs>
    <outputs>

        <data name="output" format="tabular" label="${tool.name} on ${on_string}: Classification"/>
        <!--<data format="tabular" label="${tool.name} on ${on_string}: Translated classification" name="translated" />-->
    </outputs>

    <tests>
        <test expect_num_outputs="1">
            <param name="single_paired_selector" value="no"/>
            <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/>
            <param name="split_reads" value="false"/>
            <param name="quick" value="no"/>
            <param name="only-classified-output" value="false"/>
            <param name="kraken_database" value="old_style_test_entry"/>
            <output name="output" file="kraken/kraken_test1_output.tab" ftype="tabular"/>
        </test>
        <test expect_num_outputs="1">
            <param name="single_paired_selector" value="no"/>
            <param name="input_sequences" value="kraken/kraken_test1.fa" ftype="fasta"/>
            <param name="split_reads" value="false"/>
            <param name="quick" value="no"/>
            <param name="only-classified-output" value="false"/>