comparison crossmap_vcf.xml @ 7:71730c177cdf draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit f436317e2f8d451621e297cfc474e43c20d60bb7"

6:b21851ddcc79

<tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@">
    <description>Convert genome coordinates or annotation files between genome assemblies</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    '${seq_source.chain_source.input_chain}'
#end if

'${input_file}'
'${seq_source.input_fasta}'

output
    ]]></command>

    <inputs>
        <conditional name="seq_source">

                <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/>

                <expand macro="chain" />
            </when>
        </conditional>
    </inputs>

    <outputs>
        <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output" />
        <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap" />

            <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>

            <output name="output">
                <assert_contents>
                    <has_text text="##fileformat=VCFv4.2"/>
                    <has_text text="##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)"/>
                    <has_text text="##new_reference_genome="/>
                    <has_text text="#CHROM"/>
                    <has_text_matching expression="2.*?rs11449.*?PASS"/>
                    <has_text_matching expression="2.*?rs84825.*?PASS"/>
                </assert_contents>
            </output>

7:71730c177cdf

<tool id="crossmap_vcf" name="CrossMap VCF" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.05">
    <description>Convert genome coordinates or annotation files between genome assemblies</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

    '${seq_source.chain_source.input_chain}'
#end if

'${input_file}'
'${seq_source.input_fasta}'
$no_comp_alleles
output
    ]]></command>

    <inputs>
        <conditional name="seq_source">

                <param name="input_fasta" type="data" format="fasta" label="Full genome FASTA file"/>

                <expand macro="chain" />
            </when>
        </conditional>
        <param argument="--no-comp-alleles" type="boolean" truevalue="" falsevalue="--no-comp-alleles" checked="true" label="Check if the reference allele is different from the alternate allele"/>
    </inputs>

    <outputs>
        <data name="output" format="vcf" label="${tool.name} on ${on_string}" from_work_dir="output" />
        <data name="output_unmapped" format="vcf" label="${tool.name} (unmapped) on ${on_string}" from_work_dir="output.unmap" />

            <param name="input_chain" value="test_vcf_01.over.chain" ftype="csv"/>

            <output name="output">
                <assert_contents>
                    <has_text text="##fileformat=VCFv4.2"/>
                    <has_text_matching expression="##liftOverProgram=&lt;CrossMap,version=[0-9.]+,website=https://sourceforge.net/projects/crossmap&gt;"/>
                    <has_text text="##targetRefGenome="/>
                    <has_text text="#CHROM"/>
                    <has_text_matching expression="2.*?rs11449.*?PASS"/>
                    <has_text_matching expression="2.*?rs84825.*?PASS"/>
                </assert_contents>
            </output>