comparison bcftools_convert_from_vcf.xml @ 5:2c5a7bd98c81 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e

4:8714c1caa3ee

        </xml>
        <xml name="macro_haploid2diploid">
            <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false" 
                   label="convert haploid genotypes to diploid homozygotes"  help="(\-\-haploid2diploid)"/>
        </xml>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
@PREPARE_INPUT_FILE@
#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@

bcftools @EXECUTABLE@

#if $convert.convert_to == 'gen_sample':
--tag $convert.tag $convert.chrom $convert.vcf_ids

--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

## VCF input section
#set $section = $sec_restrict
@INCLUDE@
@EXCLUDE@

## Primary Input/Outputs
"$input_file" .
]]>
    </command>
    <inputs>
        <expand macro="macro_input" />
        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_regions" />
            <expand macro="macro_targets" />

                    -->
                </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"/>
            </when>
            <when value="hap_sample">
                <expand macro="macro_haploid2diploid"/>
                <expand macro="macro_vcf_ids"/>
            </when>
            <when value="hap_legend_sample">
                <expand macro="macro_haploid2diploid"/>
                <expand macro="macro_vcf_ids"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_gen" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.gen">

5:2c5a7bd98c81

        </xml>
        <xml name="macro_haploid2diploid">
            <param name="haploid2diploid" type="boolean" truevalue="--haploid2diploid" falsevalue="" checked="false" 
                   label="convert haploid genotypes to diploid homozygotes"  help="(\-\-haploid2diploid)"/>
        </xml>
        <xml name="macro_sexinfo">
            <conditional name="sex_info">
                <param name="sex_info_src" type="select" label="sex column">
                    <help><![CDATA[
SampleName SexDesignation:
<br>MaleSample    M
<br>FemaleSample  F
                    ]]></help>
                    <option value="none">None</option>
                    <option value="history">designations from history dataset</option>
                    <option value="entry">designations from text input</option>
                </param>
                <when value="none"/>
                <when value="history">
                    <param name="sex_info_file" type="data" format="tabular" label="per sample sex designation file"/>
                </when>
                <when value="entry">
                    <param name="sex_info_lines" type="text" area="True" label="per sample sex designation" >
                        <validator type="regex" message="sample M or F separated by TAB">^(\S+[ \t][MF](\n\S+[ \t][MF])*)$</validator>
                        <sanitizer sanitize="False"/>
                    </param>
                </when>
            </conditional>
        </xml>
        <token name="@SAMPLE_SEX@">
#if $convert.sex_info.sex_info_src == 'entry':
  --sex "$entered_sex_file"
#elif $convert.sex_info.sex_info_src == 'history':
  --sex "$convert.sex_info.sex_info_file"
#end if
        </token>
    </macros>
    <expand macro="requirements" />
    <expand macro="version_command" />
    <command detect_errors="aggressive"><![CDATA[
@PREPARE_ENV@
@PREPARE_INPUT_FILE@
#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@
@PREPARE_REGIONS_FILE@

bcftools @EXECUTABLE@

#if $convert.convert_to == 'gen_sample':
--tag $convert.tag $convert.chrom $convert.vcf_ids

--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@

## Primary Input/Outputs
"$input_file" .
]]>
    </command>
    <configfiles>
        <configfile name="entered_sex_file"><![CDATA[#slurp
#if $convert.sex_info.sex_info_src == 'entry':
$convert.sex_info.sex_info_lines.__str__.strip().replace(' ','\t')#slurp
#end if]]></configfile>
    </configfiles>
    <inputs>
        <expand macro="macro_input" />
        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_regions" />
            <expand macro="macro_targets" />

                    -->
                </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"/>
                <expand macro="macro_vcf_ids"/>
                <expand macro="macro_sexinfo"/>
            </when>
            <when value="hap_legend_sample">
                <expand macro="macro_haploid2diploid"/>
                <expand macro="macro_vcf_ids"/>
                <expand macro="macro_sexinfo"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_gen" format="tabular" label="${input_file.name.rsplit('.',1)[0]}.gen">