comparison bcftools_norm.xml @ 17:48291658fdf6 draft

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

16:021693fdadaa

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
    <description>Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows</description>
    <macros>
        <token name="@EXECUTABLE@">norm</token>
        <import>macros.xml</import>
    </macros>

--check-ref $check_ref
$normalize_indels
#if $rm_dup:
  --rm-dup "$rm_dup"
#end if
#if $multiallelics.mode:
  --multiallelics '${multiallelics.mode}${multiallelics.multiallelic_types}'
#end if
#if $multiallelics.mode == '+':
  ${multiallelics.strict_filter}
#end if
#if $sec_default.site_win:
  --site-win ${sec_default.site_win}
#end if

#set $section = $sec_restrict

            <option value="w">ignore the problem (-w)</option>
            <option value="wx">exclude the variant record from the output (-wx)</option>
            <option value="ws">fix the variant record using the reference genome information (-ws)</option>
            <option value="e">exit with an error (-e)</option>
        </param>
        <param argument="--do-not-normalize" name="normalize_indels" type="boolean" truevalue="" falsevalue="--do-not-normalize" checked="false"
        label="Left-align and normalize indels?" />
        <param name="rm_dup" type="select" display="radio"
        label="Perform deduplication for the folowing types of variant records">
            <option value="">do not deduplicate any records</option>
            <option value="snps">snps</option>
            <option value="indels">indels</option>

            </when>
        </conditional>
        <section name="sec_restrict" expanded="false" title="Restrict all operations to">
            <expand macro="macro_restrict" type="region" label_type="Region" />
            <expand macro="macro_restrict" type="target" label_type="Target">
              <expand macro="macro_invert_targets" />
            </expand>
        </section>

        <section name="sec_default" expanded="false" title="Other Options">
            <param name="site_win" type="integer" label="Site Window" value="1000" optional="True" 

                    <has_text_matching expression="2\t101\t.\tA\tc\t999\tPASS"/>
                    <has_text_matching expression="2\t105\t.\tT\t&lt;DEL&gt;\t999\tPASS"/>
                </assert_contents>
            </output>
        </test>

    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@
=====================================

17:48291658fdf6

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Left-align and normalize indels; check if REF alleles match the reference; split multiallelic sites into multiple rows; recover multiallelics from multiple rows</description>
    <macros>
        <token name="@EXECUTABLE@">norm</token>
        <import>macros.xml</import>
    </macros>

--check-ref $check_ref
$normalize_indels
#if $rm_dup:
  --rm-dup "$rm_dup"
#end if
$atomize
#if $old_rec_tag
  --old-rec-tag '$old_rec_tag'
#end if
#if $multiallelics.mode:
  --multiallelics '${multiallelics.mode}${multiallelics.multiallelic_types}'
#end if
#if $multiallelics.mode == '+':
  ${multiallelics.strict_filter}
#end if

#if $sec_default.site_win:
  --site-win ${sec_default.site_win}
#end if

#set $section = $sec_restrict

            <option value="w">ignore the problem (-w)</option>
            <option value="wx">exclude the variant record from the output (-wx)</option>
            <option value="ws">fix the variant record using the reference genome information (-ws)</option>
            <option value="e">exit with an error (-e)</option>
        </param>
        <param argument="--atomize" type="boolean" truevalue="--atomize" falsevalue="" checked="false" 
            label="Atomize" help="Decompose complex variants (e.g. MNVs become consecutive SNVs)" />
        <param argument="--do-not-normalize" name="normalize_indels" type="boolean" truevalue="" falsevalue="--do-not-normalize" checked="false"
        label="Left-align and normalize indels?" />
        <param argument="--old-rec-tag" type="text" value="" optional="true" label="Annotate modified records with INFO/STR indicating the original variant">
            <sanitizer invalid_char="">
                <valid initial="string.letters,string.digits">
                    <add value="_" />
                    <add value="/" />
                </valid>
            </sanitizer>
            <validator type="regex">[0-9a-zA-Z_/]+</validator>
        </param>
        <param name="rm_dup" type="select" display="radio"
        label="Perform deduplication for the folowing types of variant records">
            <option value="">do not deduplicate any records</option>
            <option value="snps">snps</option>
            <option value="indels">indels</option>

            </when>
        </conditional>
        <section name="sec_restrict" expanded="false" title="Restrict all operations to">
            <expand macro="macro_restrict" type="region" label_type="Region" />
            <expand macro="macro_restrict" type="target" label_type="Target">
                <expand macro="macro_invert_targets" />
            </expand>
        </section>

        <section name="sec_default" expanded="false" title="Other Options">
            <param name="site_win" type="integer" label="Site Window" value="1000" optional="True" 

                    <has_text_matching expression="2\t101\t.\tA\tc\t999\tPASS"/>
                    <has_text_matching expression="2\t105\t.\tT\t&lt;DEL&gt;\t999\tPASS"/>
                </assert_contents>
            </output>
        </test>
        
        <!-- Test atomize option -->
        <test>
            <param name="input_file" ftype="vcf" value="norm.split.vcf" />
            <expand macro="test_using_reference" ref="norm.fa" />
            <param name="normalize_indels" value="true" />
            <conditional name="multiallelics">
                <param name="mode" value="-" />
            </conditional>
            <param name="atomize" value="true"/>
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <not_has_text text="TAA,TAACCCTAAA" />
                    <has_text_matching expression="1\t105\t.\tTAAACCCTA\tT\t"/>
                    <has_text_matching expression="1\t105\t.\tTA\tT\t"/>
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--atomize" />
            </assert_command>
        </test>
        <!-- Test region overlap options -->
        <test>
            <param name="input_file" ftype="vcf" dbkey="?" value="norm.vcf" />
            <expand macro="test_using_reference" select_from="cached" ref="norm" />
            <param name="normalize_indels" value="true" />
            <param name="output_type" value="v" />
            <section name="sec_restrict">
                <param name="regions_overlap" value="1"/>
            </section>
            <output name="output_file">
                <assert_contents>
                    <has_text text="T,TAACCCTA" />
                    <not_has_text text="TAA,TAACCCTAAA" />
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--regions-overlap" />
            </assert_command>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@
=====================================