comparison bowtie2_wrapper.xml @ 31:f66e4858ca26 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bowtie2 commit 30058304dcfa992f24eb7a0bdf81b280a69bea03

30:2f3400246bfc

<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy0" profile="20.05">
    <description>- map reads against reference genome</description>
    <xrefs>
        <xref type="bio.tools">bowtie2</xref>
    </xrefs>
    <macros>
        <import>bowtie2_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
        <requirement type="package" version="1.14">samtools</requirement>
    </requirements>
    <version_command>bowtie2 --version</version_command>

            <param name="analysis_type_selector" value="simple"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
        </test>
        <test expect_num_outputs="3">
            <!-- test on list paired collection -->
            <param name="type" value="paired_collection"/>
            <param name="paired_options_selector" value="no"/>

                    <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
                    <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
                </collection>
            </param>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on paired-end datasets with read group info -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="PL" value="CAPILLARY"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4"/>
        </test>
        <test expect_num_outputs="2">
            <!-- test on paired-end datasets with stats output -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <param name="save_mapping_stats" value="true" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
            <output name="mapping_stats">
                <assert_contents>
                    <has_text text="of these" />
                </assert_contents>
            </output>

            <param name="ID" value="rg1"/>
            <param name="PL" value="CAPILLARY"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fastqsanger.gz paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="analysis_type_selector" value="simple"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
            <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fastqsanger.bz2 paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="analysis_type_selector" value="simple"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
            <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fasta paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="analysis_type_selector" value="simple"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fasta paired-end datasets with bam_native as output -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <param name="sam_options_selector" value="yes" />
            <param name="reorder" value="true" />
            <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" compare="sim_size"/>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fasta paired-end datasets with sam as output -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <param name="sam_options_selector" value="yes" />
            <param name="sam_options|sam_opt" value="true" />
            <output name="output" ftype="sam">
                <assert_contents>
                    <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" />
                </assert_contents>
            </output>
        </test>

31:f66e4858ca26

<tool id="bowtie2" name="Bowtie2" version="@TOOL_VERSION@+galaxy1" profile="20.05">
    <description>- map reads against reference genome</description>
    <macros>
        <import>bowtie2_macros.xml</import>
    </macros>
    <xrefs>
        <xref type="bio.tools">bowtie2</xref>
    </xrefs>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">bowtie2</requirement>
        <requirement type="package" version="1.14">samtools</requirement>
    </requirements>
    <version_command>bowtie2 --version</version_command>

            <param name="analysis_type_selector" value="simple"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
                <metadata name="sort_order" value="coordinate"/>
            </output>
        </test>
        <test expect_num_outputs="3">
            <!-- test on list paired collection -->
            <param name="type" value="paired_collection"/>
            <param name="paired_options_selector" value="no"/>

                    <element name="forward" value="bowtie2-fq1.fq" ftype="fastqsanger" />
                    <element name="reverse" value="bowtie2-fq2.fq" ftype="fastqsanger" />
                </collection>
            </param>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
                <metadata name="sort_order" value="coordinate"/>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- test on paired-end datasets with read group info -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="PL" value="CAPILLARY"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test2.bam" ftype="bam" lines_diff="4" sort="true">
                <metadata name="sort_order" value="coordinate"/>
            </output>
        </test>
        <test expect_num_outputs="2">
            <!-- test on paired-end datasets with stats output -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fq" ftype="fastqsanger"/>
            <param name="input_2" value="bowtie2-fq2.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <param name="save_mapping_stats" value="true" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
                <metadata name="sort_order" value="coordinate"/>
            </output>
            <output name="mapping_stats">
                <assert_contents>
                    <has_text text="of these" />
                </assert_contents>
            </output>

            <param name="ID" value="rg1"/>
            <param name="PL" value="CAPILLARY"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq_il.fq" ftype="fastqsanger"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test_il.bam" ftype="bam" lines_diff="4" sort="true">
                <metadata name="sort_order" value="coordinate"/>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fastqsanger.gz paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="analysis_type_selector" value="simple"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fq.gz" ftype="fastqsanger.gz"/>
            <param name="input_2" value="bowtie2-fq2.fq.gz" ftype="fastqsanger.gz"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
                <metadata name="sort_order" value="coordinate"/>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fastqsanger.bz2 paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="analysis_type_selector" value="simple"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fq.bz2" ftype="fastqsanger.bz2"/>
            <param name="input_2" value="bowtie2-fq2.fq.bz2" ftype="fastqsanger.bz2"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test1.bam" ftype="bam" lines_diff="4" sort="true">
                <metadata name="sort_order" value="coordinate"/>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fasta paired-end datasets -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="analysis_type_selector" value="simple"/>
            <param name="source" value="history" />
            <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <output name="output" file="bowtie2-test_fasta_in.bam" ftype="bam" lines_diff="4" sort="true">
                <metadata name="sort_order" value="coordinate"/>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fasta paired-end datasets with bam_native as output -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="input_1" value="bowtie2-fq1.fa" ftype="fasta"/>
            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <param name="sam_options_selector" value="yes" />
            <param name="reorder" value="true" />
            <output name="output" file="bowtie2-test_fasta_in_bam_qname_input_sorted.bam" ftype="qname_input_sorted.bam" lines_diff="4">
                <metadata name="sort_order" value="unsorted"/>
            </output>
        </test>
        <test expect_num_outputs="1">
            <!-- test on fasta paired-end datasets with sam as output -->
            <param name="type" value="paired"/>
            <param name="paired_options_selector" value="no"/>

            <param name="input_2" value="bowtie2-fq2.fa" ftype="fasta"/>
            <param name="own_file" value="bowtie2-ref.fasta" />
            <param name="sam_options_selector" value="yes" />
            <param name="sam_options|sam_opt" value="true" />
            <output name="output" ftype="sam">
                <metadata name="sort_order" value="unsorted"/>
                <assert_contents>
                    <has_text text="M01368:8:000000000-A3GHV:1:1101:6911:8255" />
                </assert_contents>
            </output>
        </test>