comparison optitype.xml @ 2:bf36e0afdfb4 draft default tip

"planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/optitype commit 703114ab7ad18b1b0e824b103f1df213448c6e97-dirty"

1:54c9c71dabe8

<tool id="optitype" name="OptiType" version="1.3.2">
    <description>HLA genotyping predictions from NGS data</description>
    <requirements>
        <requirement type="package" version="1.3.2">optitype</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[
#set $fastqs = []
#if str( $fastq_input.fastq_input_selector ) == "paired":
    ln -s "${fastq_input.fastq_input1}" reads_1.fastq
    && ln -s "${fastq_input.fastq_input2}" reads_2.fastq
    #set $fastqs = ['reads_1.fastq','reads_2.fastq']
#elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
    ln -s "${fastq_input.fastq_input1.forward}" reads_1.fastq
    && ln -s "${fastq_input.fastq_input1.reverse}" reads_2.fastq
    #set $fastqs = ['reads_1.fastq','reads_2.fastq']
#elif str( $fastq_input.fastq_input_selector ) == "single":
    ln -s "${fastq_input.fastq_input1}" reads.fastq
    #set $fastqs = ['reads.fastq']
#end if
&& RAZERS3=`which razers3`
&& sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\$GALAXY_SLOTS/" > config.ini
#set $input_fq = ' '.join($fastqs)
&& OptiTypePipeline.py 
$read_type --input    ${' '.join($fastqs)}
#if str($beta) != '': 
 --beta $beta
#end if
#if str($enumerations) != '': 
 --enumerate $enumerations

            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="paired"/>
                <param name="fastq_input1" ftype="fastqsanger" value="rna/CRC_81_N_1_fished.fastq"/>
                <param name="fastq_input2" ftype="fastqsanger" value="rna/CRC_81_N_2_fished.fastq"/>
            </conditional>
            <output name="result">
                <assert_contents>
                    <has_text text="A*31:01" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>

2:bf36e0afdfb4

<tool id="optitype" name="OptiType" version="1.3.5">
    <description>HLA genotyping predictions from NGS data</description>
    <requirements>
        <requirement type="package" version="1.3.5">optitype</requirement>
    </requirements>
    <command detect_errors="aggressive">
<![CDATA[
#set $fastqs = []
#if str( $fastq_input.fastq_input_selector ) == "paired":
    ln -s '${fastq_input.fastq_input1}' reads_1.fastq
    && ln -s '${fastq_input.fastq_input2}' reads_2.fastq
    #set $fastqs = ['reads_1.fastq','reads_2.fastq']
#elif str( $fastq_input.fastq_input_selector ) == "paired_collection":
    ln -s '${fastq_input.fastq_input1.forward}' reads_1.fastq
    && ln -s '${fastq_input.fastq_input1.reverse}' reads_2.fastq
    #set $fastqs = ['reads_1.fastq','reads_2.fastq']
#elif str( $fastq_input.fastq_input_selector ) == "single":
    ln -s '${fastq_input.fastq_input1}' reads.fastq
    #set $fastqs = ['reads.fastq']
#end if
&& RAZERS3=`which razers3`
&& sed "s#path_to_razers3#\$RAZERS3#" '$optitype_config' | sed "s/threads=16/threads=\${GALAXY_SLOTS}/" > config.ini
#set $input_fq = ' '.join($fastqs)
&& OptiTypePipeline.py 
$read_type --input ${' '.join($fastqs)}
#if str($beta) != '': 
 --beta $beta
#end if
#if str($enumerations) != '': 
 --enumerate $enumerations

            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="paired"/>
                <param name="fastq_input1" ftype="fastqsanger" value="rna/CRC_81_N_1_fished.fastq"/>
                <param name="fastq_input2" ftype="fastqsanger" value="rna/CRC_81_N_2_fished.fastq"/>
            </conditional>
            <param name="read_type" value="--rna"/>
            <output name="result">
                <assert_contents>
                    <has_text text="A*31:01" />
                </assert_contents>
            </output>
        </test>
        <test>
            <conditional name="fastq_input">
                <param name="fastq_input_selector" value="paired"/>
                <param name="fastq_input1" ftype="fastqsanger" value="exome/NA11995_SRR766010_1_fished.fastq"/>
                <param name="fastq_input2" ftype="fastqsanger" value="exome/NA11995_SRR766010_2_fished.fastq"/>
            </conditional>
            <param name="read_type" value="--dna"/>
            <param name="unpaired_weight" value="0.2"/>
            <output name="result">
                <assert_contents>
                    <has_text text="A*01:01" />
                </assert_contents>
            </output>
        </test>
    </tests>
    <help>