comparison freebayes.xml @ 29:156b60c1530f draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freebayes commit 99e8a87a2993ae644df15756044a40a42aa7a05b

28:977a5301b66d

<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-1">
    <description>bayesian genetic variant detector</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="4.1.3">gawk</requirement>
        <requirement type="package" version="20160622">parallel</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

            <param name="reference_source_selector" value="history" />
            <param name="processmode" value="individual" />
            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
            <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
            <param name="options_type_selector" value="simple"/>
            <output name="output_vcf" file="freebayes-phix174-test1.vcf" compare="contains"/>
        </test>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="processmode" value="individual" />
            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
            <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
            <param name="options_type_selector" value="naive_w_filters"/>
            <param name="min_coverage" value="14"/>
            <output name="output_vcf" file="freebayes-phix174-test2.vcf" compare="contains"/>
        </test>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="processmode" value="individual" />
            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
            <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
            <param name="options_type_selector" value="naive_w_filters"/>
            <param name="min_coverage" value="14"/>
            <output name="output_vcf" file="freebayes-phix174-test3.vcf" compare="contains"/>
        </test>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="processmode" value="individual" />
            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
            <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
            <param name="options_type_selector" value="full"/>
            <param name="population_model_selector" value="set"/>
            <param name="P" value="1"/>
            <output name="output_vcf" file="freebayes-phix174-test4.vcf" compare="contains"/>
        </test>
    </tests>
    <help>
**What it does**

**Acknowledgments**

The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
TNG was developed by Bjoern Gruening.
    </help>
    <expand macro="citations" />
</tool>

29:156b60c1530f

<tool id="freebayes" name="FreeBayes" version="@DEPENDENCY_VERSION@-0">
    <description>bayesian genetic variant detector</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="4.1.3">gawk</requirement>
        <requirement type="package" version="20170422">parallel</requirement>
    </expand>
    <command detect_errors="exit_code"><![CDATA[
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

            <param name="reference_source_selector" value="history" />
            <param name="processmode" value="individual" />
            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
            <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
            <param name="options_type_selector" value="simple"/>
            <output name="output_vcf" file="freebayes-phix174-test1.vcf" lines_diff="4" />
        </test>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="processmode" value="individual" />
            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
            <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
            <param name="options_type_selector" value="naive_w_filters"/>
            <param name="min_coverage" value="14"/>
            <output name="output_vcf" file="freebayes-phix174-test2.vcf" lines_diff="4" />
        </test>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="processmode" value="individual" />
            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
            <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
            <param name="options_type_selector" value="naive_w_filters"/>
            <param name="min_coverage" value="14"/>
            <output name="output_vcf" file="freebayes-phix174-test3.vcf" lines_diff="4" />
        </test>
        <test>
            <param name="reference_source_selector" value="history" />
            <param name="processmode" value="individual" />
            <param name="ref_file" ftype="fasta" value="freebayes-phix174.fasta"/>
            <param name="input_bams" ftype="bam" value="freebayes-phix174.bam"/>
            <param name="options_type_selector" value="full"/>
            <param name="population_model_selector" value="set"/>
            <param name="P" value="1"/>
            <output name="output_vcf" file="freebayes-phix174-test4.vcf" lines_diff="4" />
        </test>
    </tests>
    <help>
**What it does**

**Acknowledgments**

The initial version of the wrapper was produced by Dan Blankenberg and upgraded by Anton Nekrutenko.
TNG was developed by Bjoern Gruening.
    </help>
    <expand macro="citations">
        <citation type="bibtex">
            @article{Tange2011a,
                title = {GNU Parallel - The Command-Line Power Tool},
                author = {O. Tange},
                address = {Frederiksberg, Denmark},
                journal = {;login: The USENIX Magazine},
                month = {Feb},
                number = {1},
                volume = {36},
                url = {http://www.gnu.org/s/parallel},
                year = {2011},
                pages = {42-47}
            }
        </citation>
    </expand>
</tool>