comparison crossmap_vcf.xml @ 11:b17b9f3a148a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit ad4d739b4837dd61abc85614568d22f271f14568

10:1e9997ca9e14

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>

    <command detect_errors="aggressive"><![CDATA[
#set $input_file = str($seq_source.input)

ln -s '${seq_source.input_fasta}' 'genome.fasta' &&

CrossMap.py vcf

#if $seq_source.index_source_s == "cached"
    ## This is the 2nd dbkey, and the corresponding value has to be looked up
    "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
#else

'${input_file}'
'genome.fasta'
$no_comp_alleles
output
    ]]></command>

    <inputs>
        <conditional name="seq_source">
            <param name="index_source_s" type="select" label="Source for Input Data">
                <option value="cached">Local data (in galaxy)</option>
                <option value="history">From History</option>

                    -->
                </param>
                <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
                    <options from_data_table="all_fasta"/>
                </param>

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

            <when value="history">
                <param name="input" type="data" format="vcf" label="VCF file"/>
                <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" />
    </outputs>

    <tests>
        <test>
            <param name="index_source_s" value="history"/>
            <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
            <param name="index_source" value="history"/>
            <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
            <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>

  not indexed, CrossMap will automatically indexed it (only the first time
  you run CrossMap).
- In the output VCF file, whether the chromosome IDs contain “chr” or not
  depends on the format of the input VCF file.
    ]]></help>

    <citations>
        <citation type="doi">10.1093/bioinformatics/btt730</citation>
    </citations>
</tool>

11:b17b9f3a148a

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
#set $input_file = str($seq_source.input)

ln -s '${seq_source.input_fasta}' 'genome.fasta' &&

CrossMap vcf

#if $seq_source.index_source_s == "cached"
    ## This is the 2nd dbkey, and the corresponding value has to be looked up
    "${filter(lambda x: str( x[1] ) == str($seq_source.chain_source.input_chain ), $__app__.tool_data_tables['liftOver'].get_fields())[0][2] }"
#else

'${input_file}'
'genome.fasta'
$no_comp_alleles
output
    ]]></command>
    <inputs>
        <conditional name="seq_source">
            <param name="index_source_s" type="select" label="Source for Input Data">
                <option value="cached">Local data (in galaxy)</option>
                <option value="history">From History</option>

                    -->
                </param>
                <param name="input_fasta" type="select" label="Lift Over To (FASTA file)" help="The FASTA file must be on the same build (dbkey) as the LiftOver chain file">
                    <options from_data_table="all_fasta"/>
                </param>
                <expand macro="chain"/>
            </when>
            <when value="history">
                <param name="input" type="data" format="vcf" label="VCF file"/>
                <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"/>
    </outputs>
    <tests>
        <test>
            <param name="index_source_s" value="history"/>
            <param name="input" value="test_vcf_01_input.vcf" ftype="vcf"/>
            <param name="index_source" value="history"/>
            <param name="input_fasta" value="test_vcf_01.fasta" ftype="fasta"/>
            <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=CrossMap,version=[0-9.]+,website=https://crossmap.readthedocs.io/en/latest"/>
                    <has_text text="##targetRefGenome="/>
                    <has_text text="#CHROM"/>
                    <has_text_matching expression="2.*?rs11449.*?PASS"/>
                    <has_text_matching expression="2.*?rs84825.*?PASS"/>
                </assert_contents>

  not indexed, CrossMap will automatically indexed it (only the first time
  you run CrossMap).
- In the output VCF file, whether the chromosome IDs contain “chr” or not
  depends on the format of the input VCF file.
    ]]></help>
    <citations>
        <citation type="doi">10.1093/bioinformatics/btt730</citation>
    </citations>
</tool>