comparison bcftools_convert_from_vcf.xml @ 16:9b29129fb491 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49

15:1137ce8efc1e

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@ from vcf" id="bcftools_@EXECUTABLE@_from_vcf" version="@TOOL_VERSION@">
    <description>Converts VCF/BCF to IMPUTE2/SHAPEIT formats</description>
    <macros>
        <token name="@EXECUTABLE@">convert</token>
        <import>macros.xml</import>
        <xml name="macro_vcf_ids">

@PREPARE_REGIONS_FILE@

bcftools @EXECUTABLE@

#if $convert.convert_to == 'gen_sample':
--tag $convert.tag $convert.chrom $convert.vcf_ids
--gensample "$output_gen,$output_samples"
#elif $convert.convert_to == 'hap_sample':
$convert.vcf_ids $convert.haploid2diploid
--hapsample "$output_hap,$output_samples"
#elif $convert.convert_to == 'hap_legend_sample':
$convert.vcf_ids $convert.haploid2diploid
--haplegendsample "$output_hap,$output_legend,$output_samples"
#end if
@SAMPLE_SEX@

## VCF input section
#set $section = $sec_restrict
@INCLUDE@
@EXCLUDE@
@REGIONS@
@TARGETS@
@SAMPLES@

## Primary Input/Outputs
"$input_file" .
]]>
    </command>

            <expand macro="macro_restrict" type="target" label_type="Target" />
            <expand macro="macro_samples" />
            <expand macro="macro_include" />
            <expand macro="macro_exclude" />
        </section>
        <conditional name="convert">
            <param name="convert_to" type="select" label="convert to">
                <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option>
                <option value="hap_sample">hap sample - IMPUTE2 or SHAPEIT</option>
                <option value="hap_legend_sample">hap legend sample - IMPUTE2 or SHAPEIT</option>

                    <option value="GP">GP</option>
                    <!--
                    <option value="GL">GL</option>
                    -->
                </param>
                <param name="chrom" type="boolean" truevalue="--chrom" falsevalue="" checked="false" 
                   label="Output chromosome in first column instead of CHROM:POS_REF_ALT" help="(\-\-chrom)"/>
                <expand macro="macro_vcf_ids"/>
                <expand macro="macro_sexinfo"/>
            </when>
            <when value="hap_sample">
                <expand macro="macro_haploid2diploid"/>

        </test>
        <test>
            <param name="input_file" ftype="vcf" value="convert.vcf" />
            <param name="convert_to"  value="gen_sample" />
            <param name="tag"  value="GP" />
            <param name="chrom"  value="True" />
            <output name="output_gen">
                <assert_contents>
                    <has_text text="X X:2698560_G_A 2698560 G A 1.00"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="check.vcf" />
            <param name="convert_to"  value="gen_sample" />
            <param name="tag"  value="GT" />
            <param name="chrom"  value="True" />
            <param name="vcf_ids"  value="True" />
            <output name="output_gen">
                <assert_contents>
                    <has_text text="1 id3D 3062915 GTTT G 0 1 0 0 1 0"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="convert.vcf" />

                <assert_contents>
                    <has_text text="sample population group sex"/>
                    <has_text text="NA00001 NA00001 NA00001 2"/>
                </assert_contents>
            </output>
        </test>
    </tests>

    <help><![CDATA[
=====================================

16:9b29129fb491

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@ from vcf" id="bcftools_@EXECUTABLE@_from_vcf" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Converts VCF/BCF to IMPUTE2/SHAPEIT formats</description>
    <macros>
        <token name="@EXECUTABLE@">convert</token>
        <import>macros.xml</import>
        <xml name="macro_vcf_ids">

@PREPARE_REGIONS_FILE@

bcftools @EXECUTABLE@

#if $convert.convert_to == 'gen_sample':
--tag $convert.tag $convert.convert_3N6 $convert.vcf_ids ## chrom option has been deprecated
--gensample "$output_gen,$output_samples"
#elif $convert.convert_to == 'hap_sample':
$convert.vcf_ids $convert.haploid2diploid
--hapsample "$output_hap,$output_samples"
#elif $convert.convert_to == 'hap_legend_sample':
$convert.vcf_ids $convert.haploid2diploid
--haplegendsample "$output_hap,$output_legend,$output_samples"
#end if
@SAMPLE_SEX@

#if $keep_duplicates
    --keep-duplicates $keep_duplicates
#end if

## VCF input section
#set $section = $sec_restrict
@INCLUDE@
@EXCLUDE@
@REGIONS@
@TARGETS@
@SAMPLES@


## Primary Input/Outputs
"$input_file" .
]]>
    </command>

            <expand macro="macro_restrict" type="target" label_type="Target" />
            <expand macro="macro_samples" />
            <expand macro="macro_include" />
            <expand macro="macro_exclude" />
        </section>
        <param argument="--keep-duplicates" type="boolean" truevalue="--keep-duplicates" falsevalue="" checked="false" label="Keep duplicates" help="Keep all multiallelic variants" />
        <conditional name="convert">
            <param name="convert_to" type="select" label="convert to">
                <option value="gen_sample">gen sample - IMPUTE2 or SHAPEIT</option>
                <option value="hap_sample">hap sample - IMPUTE2 or SHAPEIT</option>
                <option value="hap_legend_sample">hap legend sample - IMPUTE2 or SHAPEIT</option>

                    <option value="GP">GP</option>
                    <!--
                    <option value="GL">GL</option>
                    -->
                </param>
                <param name="convert_3N6" argument="--3N6" type="boolean" truevalue="--3N6" falsevalue="" checked="false" label="3N6 format" help="Use 3N+6 column format instead of the old 3N+5 column format" />
                <expand macro="macro_vcf_ids"/>
                <expand macro="macro_sexinfo"/>
            </when>
            <when value="hap_sample">
                <expand macro="macro_haploid2diploid"/>

        </test>
        <test>
            <param name="input_file" ftype="vcf" value="convert.vcf" />
            <param name="convert_to"  value="gen_sample" />
            <param name="tag"  value="GP" />
            <param name="convert_3N6"  value="True" />
            <output name="output_gen">
                <assert_contents>
                    <has_text text="X:2698630_A_G X:2698630_A_G 2698630 A G 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="check.vcf" />
            <param name="convert_to"  value="gen_sample" />
            <param name="tag"  value="GT" />
            <param name="convert_3N6"  value="True" />
            <param name="vcf_ids"  value="True" />
            <output name="output_gen">
                <assert_contents>
                    <has_text text="1:3062915_GTTT_G id3D 3062915 GTTT G 0 1 0 0 1 0"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_file" ftype="vcf" value="convert.vcf" />

                <assert_contents>
                    <has_text text="sample population group sex"/>
                    <has_text text="NA00001 NA00001 NA00001 2"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test keep-duplicates option -->
        <test>
            <param name="input_file" ftype="vcf" value="convert.vcf" />
            <param name="convert_to"  value="hap_legend_sample" />
            <param name="keep_duplicates" value="true"/>
            <output name="output_hap">
                <assert_contents>
                    <has_text text="1 0 1 1 0 1 1 0 1 0 0 0 0 0 0 0 0 0 0 0"/>
                </assert_contents>
            </output>
            <output name="output_legend">
                <assert_contents>
                    <has_text text="X:2698769_AAG_A 2698769 AAG A"/>
                </assert_contents>
            </output>
            <output name="output_samples">
                <assert_contents>
                    <has_text text="sample population group sex"/>
                    <has_text text="NA00001 NA00001 NA00001 2"/>
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--keep-duplicates" />
            </assert_command>
        </test>
        <!-- Test region overlap -->
        <test>
            <param name="input_file" ftype="vcf" value="convert.vcf" />
            <param name="convert_to"  value="gen_sample" />
            <section name="sec_restrict">
                <param name="regions_overlap" value="1"/>
            </section>
            <output name="output_gen">
                <assert_contents>
                    <has_text text="X:2698560_G_A X:2698560_G_A 2698560 G A 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0 1 0 0"/>
                </assert_contents>
            </output>
            <output name="output_samples">
                <assert_contents>
                    <has_text text="NA00001 NA00001 0"/>
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--regions-overlap" />
            </assert_command>
        </test>
    </tests>

    <help><![CDATA[
=====================================