comparison crossmap.xml @ 9:0cae6e3273a8 draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/crossmap_galaxy_wrapper commit 0acafcc4ce1261ec93eee1ad209a05246f4f02fd

8:9750f8c1d3cb

        <requirement type="package" version="0.1.9">crossmap</requirement>
    </requirements>
    
    <stdio>
        <regex match="Usage: CrossMap.py" source="stdin" level="fatal"/>
        <regex match="^@ " source="stdin" level="warning" />
    </stdio>

    <command>
        CrossMap.py
            $multiple.input_format

            
            #if $multiple.input_format == "vcf"
                "$multiple.seq_source.input_fasta"
            #end if 
            
            $output
    </command>

    <inputs>
        <conditional name="multiple">
            <param name="input_format" type="select" label="Convert a file of the following format">

                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param format="bed" name="input" type="data" label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." />
                            <param type="data" name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
            </when>
            <when value="bigwig">
                <conditional name="seq_source">

            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <data format="text" name="output" label="${tool.name} on ${input.hid}: ${input.name}" />
    </outputs>
    
    <tests>
        <test>
            <param name="input" value="test1.hg19.txt"/>

9:0cae6e3273a8

        <requirement type="package" version="0.1.9">crossmap</requirement>
    </requirements>
    
    <stdio>
        <regex match="Usage: CrossMap.py" source="stdin" level="fatal"/>
        <regex match=".*" source="both" level="log" description="tool progress"/>
    </stdio>

    <command>
        CrossMap.py
            $multiple.input_format

            
            #if $multiple.input_format == "vcf"
                "$multiple.seq_source.input_fasta"
            #end if 
            
            <!-- BED format does not write to the output file, but does write fails to stdout -->
            > "$output"
            
            2>/dev/null
    </command>

    <inputs>
        <conditional name="multiple">
            <param name="input_format" type="select" label="Convert a file of the following format">

                                    <filter type="data_meta" ref="input" key="dbkey" column="0" />
                                </options>
                            </param>
                        </when>
                        <when value="history">
                            <param type="data" format="bed" name="input"       label="BED file" help="BED format file must have at least 3 columns (chrom, start, end) and no more than 12 columns." />
                            <param type="data"              name="input_chain" label="LiftOver chain file" />
                        </when>
                </conditional>
            </when>
            <when value="bigwig">
                <conditional name="seq_source">

            </when>
        </conditional>
    </inputs>
    
    <outputs>
        <data format="text" name="output" label="${tool.name} on " />
    </outputs>
    
    <tests>
        <test>
            <param name="input" value="test1.hg19.txt"/>