comparison bcftools_view.xml @ 14:11f6245358e6 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 8f0dacb44516206751262495e6a6de22ae312572"

13:5e2c39218cf7

  --min-ac ${section.min_ac}
#end if
#if str($section.max_ac)
  --max-ac ${section.max_ac}
#end if
#if str($section.select_genotype) != "__none__":
  --genotype "${section.select_genotype}"
#end if
## known or novel
#if $section.known_or_novel:
  ${section.known_or_novel}

        <section name="sec_filter" expanded="false" title="Filter Options">
            <param name="min_ac" type="integer" label="Min Ac" optional="True"
                   help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
            <param name="max_ac" type="integer" label="Max Ac" optional="True"
                   help="(-C --max-ac) Maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
            <param name="select_genotype" type="select">
                <option value="__none__" selected="True">No selection</option>
                <option value="require one or more hom/het/missing genotype or" />
                <option value="if prefixed with &quot;^&quot;" />
                <option value="exclude sites with hom/het/missing genotypes" />
            </param>

            <param name="types" type="select" label="Select Types"  multiple="true" optional="True">
                <help>
                 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested.
                 Types are determined by comparing the REF and ALT alleles in the VCF record.
                </help>

                    <not_has_text text="rs62584840" />
                    <has_text text="2343543" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@
=====================================

14:11f6245358e6

  --min-ac ${section.min_ac}
#end if
#if str($section.max_ac)
  --max-ac ${section.max_ac}
#end if
#if str($section.select_genotype) != "None":
  --genotype "${section.select_genotype}"
#end if
## known or novel
#if $section.known_or_novel:
  ${section.known_or_novel}

        <section name="sec_filter" expanded="false" title="Filter Options">
            <param name="min_ac" type="integer" label="Min Ac" optional="True"
                   help="(-c --min-ac) Minimum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
            <param name="max_ac" type="integer" label="Max Ac" optional="True"
                   help="(-C --max-ac) Maximum count for non-reference (nref), 1st alternate (alt1), least frequent (minor), most frequent (major) or sum of all but most frequent (nonmajor) alleles" />
            <param name="select_genotype" type="select" label="Select Genotype" optional="True">
                <help>
                Include only sites with one or more homozygous (hom), heterozygous (het) or missing (miss) genotypes.
                When prefixed with ^, the logic is reversed.
                Please notice that if the input file doesn't have any genotype columns,
                then this option is ignored altogether.
                </help>
                <option value="hom">hom</option>
                <option value="het">het</option>
                <option value="miss">miss</option>
                <option value="^hom">^hom</option>
                <option value="^het">^het</option>
                <option value="^miss">^miss</option>
            </param>
            <param name="types" type="select" label="Select Types"  multiple="true" optional="True">
                <help>
                 List of variant types to select. Site is selected if any of the ALT alleles is of the type requested.
                 Types are determined by comparing the REF and ALT alleles in the VCF record.
                </help>

                    <not_has_text text="rs62584840" />
                    <has_text text="2343543" />
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="view.vcf" />
            <param name="phased" value="--phased" />
            <param name="output_type" value="v" />
            <param name="select_genotype" value="^het" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="--genotype ^het" />
                    <has_text text="rs78249411" />
                    <not_has_text text="3048719" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@
=====================================