comparison bcftools_merge.xml @ 18:63f75c284e32 draft

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

17:45050fb22a09

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
    <description>Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file</description>
    <macros>
        <token name="@EXECUTABLE@">merge</token>
        <import>macros.xml</import>
    </macros>

  --info-rules "${section.info_rules}"
#end if

#if $section.merge:
  --merge "${section.merge}"
#end if

#set $section = $sec_restrict
@APPLY_FILTERS@
@REGIONS@

                  <option value="indels">indels - allow multiallelic indel records</option>
                  <option value="both">both - both SNP and indel records can be multiallelic</option>
                  <option value="all">all - SNP records can be merged with indel records</option>
                  <option value="id">id - merge by ID</option>
            </param>
        </section>
        <section name="sec_header" expanded="false" title="Header Options">
          <param name="use_header" type="data" format="vcf" label="Use Header" optional="True" help="Use the provided header" />
          <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header" help="Print only the merged header and exit" />
        </section>

                    <has_text_matching expression="1\t3000000\t.\tC\t(CG,CCG|CCG,CG)\t"/>
                    <has_text_matching expression="TR=[^;\t]*11"/>
                </assert_contents>
            </output>
        </test>
        <test>
            <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" />
            <param name="force_samples" value="true" />
            <param name="merge" value="id" />
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@

18:63f75c284e32

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file</description>
    <macros>
        <token name="@EXECUTABLE@">merge</token>
        <import>macros.xml</import>
    </macros>

  --info-rules "${section.info_rules}"
#end if

#if $section.merge:
  --merge "${section.merge}"
  $section.no_index
#end if

#set $section = $sec_restrict
@APPLY_FILTERS@
@REGIONS@

                  <option value="indels">indels - allow multiallelic indel records</option>
                  <option value="both">both - both SNP and indel records can be multiallelic</option>
                  <option value="all">all - SNP records can be merged with indel records</option>
                  <option value="id">id - merge by ID</option>
            </param>
            <param argument="--no-index" type="boolean" truevalue="--no-index" falsevalue="" checked="false"
                label="Allow merge unindexed files" help="Requires the input files to have chromosomes in th same order and consistent with the order of sequences in the header" />
        </section>
        <section name="sec_header" expanded="false" title="Header Options">
          <param name="use_header" type="data" format="vcf" label="Use Header" optional="True" help="Use the provided header" />
          <param name="print_header" type="boolean" truevalue="--print-header" falsevalue="" label="Print Header" help="Print only the merged header and exit" />
        </section>

                    <has_text_matching expression="1\t3000000\t.\tC\t(CG,CCG|CCG,CG)\t"/>
                    <has_text_matching expression="TR=[^;\t]*11"/>
                </assert_contents>
            </output>
        </test>
        <!-- Test no_index option -->
        <test>
            <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" />
            <param name="force_samples" value="true" />
            <param name="merge" value="id" />
            <param name="no_index" value="true"/>
            <param name="output_type" value="v" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--no-index" />
            </assert_command>
        </test>
        <!-- Test region overlap option -->
        <test>
            <param name="input_files" ftype="vcf" value="merge.4.a.vcf,merge.4.b.vcf" />
            <param name="force_samples" value="true" />
            <param name="merge" value="id" />
            <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_matching expression="1\t3000000\tid1\tC\t(A,CCG|CCG,A)\t"/>
                </assert_contents>
            </output>
            <assert_command>
                <has_text text="--regions-overlap" />
            </assert_command>
        </test>
    </tests>
    <help><![CDATA[
=====================================
 bcftools @EXECUTABLE@