comparison optitype.xml @ 5:044f0a2e2a36 draft default tip

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4:111d2508ab15

<tool id="optitype" name="OptiType" version="1.2.1">
    <description>HLA genotyping predictions from NGS data</description>
    <requirements>
        <requirement type="package" version="1.2.1">optitype</requirement>
    </requirements>
 <stdio>
         <exit_code range="1:"    level="fatal" description="Error Running optitype" />
 </stdio>
    <command>
<![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( $fastq_input.fastq_input_selector ) == "single":
    ln -s "${fastq_input.fastq_input1}" reads.fastq
    #set $fastqs = ['reads.fastq']
#end if
&& cp \$OPTITYPE_DIR/config.ini .
&& sed "s/path_to_razers3/`which razers3`/" '$optitype_config' | sed "s/threads=16/threads=\$GALAXY_SLOTS/" > config.ini
&& ln -s \$OPTITYPE_DIR/data data
#set $input_fq = ' '.join($fastqs)
&& OptiTypePipeline.py 
$read_type --input    ${' '.join($fastqs)}
#if str($beta) != '': 
 --beta $beta

5:044f0a2e2a36

<tool id="optitype" name="OptiType" version="1.2.1">
    <description>HLA genotyping predictions from NGS data</description>
    <requirements>
        <requirement type="package" version="1.2.1">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( $fastq_input.fastq_input_selector ) == "single":
    ln -s "${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