comparison seq2hla.xml @ 1:5a7cd6c39085 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/seq2hla commit c6f68e0efd9aa7e566289650ad126e0c7d192a8b"

0:52bba1cd3823

<tool id="seq2hla" name="seq2HLA" version="2.2.0">
    <description>HLA genotype and expression from RNA-seq</description>
    <requirements>
        <!-- needed because of some non POSIX compliant wc usage -->
        <requirement type="package" version="8.31">coreutils</requirement>
        <requirement type="package" version="2.2">seq2hla</requirement>

    ]]></command>
    <inputs>
        <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis">
            <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator>
        </param>
        <param name="fastq_input1" type="data" format="fastqsanger" label="Select first set of reads" help="Specify dataset with forward reads"/>
        <param name="fastq_input2" type="data" format="fastqsanger" label="Select second set of reads" help="Specify dataset with reverse reads"/>
        <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime" 
               help="trim this many bases from the low-quality end of each read" />
    </inputs>
    <outputs>
        <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/>

        <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/>
    </outputs>
    <tests>
        <test>
            <param name="run_name" value="test"/>
            <param name="fastq_input1" ftype="fastqsanger" value="reads1.fastq"/>
            <param name="fastq_input2" ftype="fastqsanger" value="reads2.fastq"/>
            <output name="c1_genotype4digits">
                <assert_contents>
                    <has_text text="A*24:02" />
                </assert_contents>
            </output>

1:5a7cd6c39085

<tool id="seq2hla" name="seq2HLA" version="2.2.0+galaxy1">
    <description>HLA genotype and expression from RNA-seq</description>
    <requirements>
        <!-- needed because of some non POSIX compliant wc usage -->
        <requirement type="package" version="8.31">coreutils</requirement>
        <requirement type="package" version="2.2">seq2hla</requirement>

    ]]></command>
    <inputs>
        <param name="run_name" type="text" value="sample1" label="Name prefix for this analysis">
            <validator type="regex" message="Use letters,digits,_.-">^[A-Za-z0-9_\-+.]+$</validator>
        </param>
        <param name="fastq_input1" type="data" format="fastqsanger,fastqsanger.gz" label="Select first set of reads" help="Specify dataset with forward reads"/>
        <param name="fastq_input2" type="data" format="fastqsanger,fastqsanger.gz" label="Select second set of reads" help="Specify dataset with reverse reads"/>
        <param name="trim" type="integer" value="" min="0" optional="true" label="Trim bases from 3 prime" 
               help="trim this many bases from the low-quality end of each read" />
    </inputs>
    <outputs>
        <data format="txt" name="seq2hla_log" label="${tool.name} on ${on_string}: ${run_name} logfile"/>

        <data format="txt" name="ambiguity" label="${tool.name} on ${on_string}: ${run_name}.ambiguity"/>
    </outputs>
    <tests>
        <test>
            <param name="run_name" value="test"/>
            <param name="fastq_input1" ftype="fastqsanger.gz" value="reads1.fastq.gz"/>
            <param name="fastq_input2" ftype="fastqsanger.gz" value="reads2.fastq.gz"/>
            <output name="c1_genotype4digits">
                <assert_contents>
                    <has_text text="A*24:02" />
                </assert_contents>
            </output>