annotate replace_chromosome_names.xml @ 1:6c0373cc070f draft default tip

planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/replace_chromosome_names/ commit c8418d1d7657dacae7f81fe4aa0aba051873d4ad

<tool id="replace_chromosome_names" name="Replace chromosome names" version="0.1">
    <description>in a tabular dataset using a mapping table</description>
    <requirements>
        <requirement type="package" version="3.6.1">python</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
python '$__tool_directory__/replace_chromosome_names.py' --cols $cols -m '$mapping' --comment-char '$comment_char' -o '$output' '$input'
    ]]></command>
    <inputs>
        <param name="input" type="data" format="tabular" label="Tabular input dataset" />
        <param name="cols" type="data_column" data_ref="input" multiple="true" label="Columns on which to perform the replacement" />
        <param name="mapping" type="data" format="tabular" label="Mapping table" help="Must contain 2 tab-separated columns" />
        <param name="comment_char" type="text" value="" label="Comment character" help="Lines starting with this character will be directly printed to the output file">
            <validator type="length" min="0" max="1" />
            <validator type="expression" message="Must be a punctuation character"><![CDATA[value in '!"#$%&\'()*+,-./:;<=>?@[\\]^_`{|}~']]></validator>
            <sanitizer>
                <valid initial="string.punctuation"/>
            </sanitizer>
        </param>
    </inputs>
    <outputs>
        <data name="output" format_source="input" label="${tool.name} on ${on_string}" />
    </outputs>
    <tests>
        <test>
            <param name="input" ftype="vcf" value="gemini_load_input.vcf" />
            <param name="cols" value="1" />
            <param name="mapping" ftype="tabular" value="GRCh37_ensembl2UCSC.txt" />
            <param name="comment_char" value="#" />
            <output name="output" ftype="vcf" file="replace_chromosome_names_output.vcf" />
            <assert_stderr>
                <has_text text="HG1007_PATCH" />
            </assert_stderr>
        </test>
    </tests>
    <help><![CDATA[
**What it does**

Replace chromosome names in a tabular (e.g. VCF) dataset using a mapping table.

Chromosome mapping tables can be downloaded from: https://github.com/dpryan79/ChromosomeMappings/
    ]]></help>
    <citations>
    </citations>
</tool>