comparison bcftools_gtcheck.xml @ 2:166520508473 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 5725fea947162618d77de7b8011d18b2f16c7094

1:d548c5551f01

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.0">
    <description>Check sample identity</description>
    <macros>
        <token name="@EXECUTABLE@">gtcheck</token>
        <import>macros.xml</import>
    </macros>

#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@
#set $section = $sec_default
#set $genotypes_vcf = None
#if $section.genotypes:
  #if $section.genotypes.datatype.file_ext == 'vcf'
    #set $genotypes_vcf = 'genotypes.vcf.gz'
    bgzip -c "$section.genotypes" > $genotypes_vcf &&
    bcftools index $genotypes_vcf &&
  #elif $section.genotypes.datatype.file_ext == 'bcf'
    #set $genotypes_vcf = 'genotypes.bcf'
    ln -s "$ection.genotypes" $genotypes_vcf && 
    #if $section.genotypes.metadata.bcf_index:
      ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
    #else 
      bcftools index $genotypes_vcf &&
    #end if
  #end if
#end if

        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_regions" />
            <expand macro="macro_targets" />
        </section>
        <section name="sec_default" expanded="true" title="Default Options">
            <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True" 
                   help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
            <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" />
            <param name="GTs_only" type="integer" label="Gts Only" default="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
            <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
            <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" />
            <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query sample (by default the first sample is checked)" />
            <param name="plot" type="text" label="Plot" help="Prefix name for plot" />
        </section>

        <data name="output_file" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="view.vcf" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="SM\t10328.0+\t80.68\t12\tNA00002\t0"/>
                    <has_text_matching expression="CN\t1174\t14\t75.57\tNA00002\tNA00001"/>
                </assert_contents>

2:166520508473

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@VERSION@.1">
    <description>Check sample identity</description>
    <macros>
        <token name="@EXECUTABLE@">gtcheck</token>
        <import>macros.xml</import>
    </macros>

#set $section = $sec_restrict
@PREPARE_TARGETS_FILE@
#set $section = $sec_default
#set $genotypes_vcf = None
#if $section.genotypes:
  #if $section.genotypes.is_of_type('vcf')
    #set $genotypes_vcf = 'genotypes.vcf.gz'
    bgzip -c "$section.genotypes" > $genotypes_vcf &&
    bcftools index $genotypes_vcf &&
  #elif $section.genotypes.is_of_type('bcf')
    #set $genotypes_vcf = 'genotypes.bcf'
    ln -s "$ection.genotypes" $genotypes_vcf &&
    #if $section.genotypes.metadata.bcf_index:
      ln -s $section.genotypes.metadata.bcf_index ${genotypes_vcf}.csi &&
    #else
      bcftools index $genotypes_vcf &&
    #end if
  #end if
#end if

        <section name="sec_restrict" expanded="false" title="Restrict to">
            <expand macro="macro_regions" />
            <expand macro="macro_targets" />
        </section>
        <section name="sec_default" expanded="true" title="Default Options">
            <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
                   help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
            <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" />
            <param name="GTs_only" type="integer" label="Gts Only" value="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
            <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
            <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" />
            <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query sample (by default the first sample is checked)" />
            <param name="plot" type="text" label="Plot" help="Prefix name for plot" />
        </section>

        <data name="output_file" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="view.vcf" />
            <param name="GTs_only" value="" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="SM\t10328.0+\t80.68\t12\tNA00002\t0"/>
                    <has_text_matching expression="CN\t1174\t14\t75.57\tNA00002\tNA00001"/>
                </assert_contents>