comparison crossmap_vcf.xml @ 4:69349b98b727 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/crossmap commit 23fab16cd40acbd5b0e9d640ed3858040db7a622

3:b878e87edb81

<tool id="crossmap_vcf" name="CrossMap VCF" version="@WRAPPER_VERSION@-0">
    <description>Convert genome coordinates or annotation files between genome assemblies</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>

#end if

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

'${output}'

&& mv '${output}.unmap' '$output_unmapped'
    ]]></command>

    <inputs>
        <conditional name="seq_source">
            <param name="index_source_s" type="select" label="Source for Input Data">

            </when>
        </conditional>
    </inputs>

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

    <tests>
        <test>
            <param name="index_source_s" value="history"/>

- If the reference genome sequence file (../database/genome/hg18.fa) was
  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>

4:69349b98b727

<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"/>

#end if

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

output
    ]]></command>

    <inputs>
        <conditional name="seq_source">
            <param name="index_source_s" type="select" label="Source for Input Data">

            </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" />
    </outputs>

    <tests>
        <test>
            <param name="index_source_s" value="history"/>

- If the reference genome sequence file (../database/genome/hg18.fa) was
  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>