comparison picard_FastqToSam.xml @ 7:08f69add4d06 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 7491208ca0c917a053798a48c3e54c3e30e95d92

6:961236c5ec73

  <description>convert Fastq data into unaligned BAM</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <stdio>
    <exit_code range="1:" level="fatal"/>
  </stdio>
  <command>
    @java_options@
    
    java -jar \$JAVA_JAR_PATH/picard.jar
    FastqToSam
    
    #if str( $input_type.input_type_selector ) == "se":
      FASTQ="${input_type.fastq}"
    #elif str( $input_type.input_type_selector ) == "pe":

    SORT_ORDER=coordinate
    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  </command>
  <inputs>
    <conditional name="input_type">
      <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types">
        <option value="se">Single end (single dataset)</option>
        <option value="pe">Paired end (two datasets)</option>

7:08f69add4d06

  <description>convert Fastq data into unaligned BAM</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    
    picard
    FastqToSam
    
    #if str( $input_type.input_type_selector ) == "se":
      FASTQ="${input_type.fastq}"
    #elif str( $input_type.input_type_selector ) == "pe":

    SORT_ORDER=coordinate
    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  ]]></command>
  <inputs>
    <conditional name="input_type">
      <param name="input_type_selector" type="select" label="What is your input data" help="Select between single end, paired end, and collections. See help below for full explanation of dataset types">
        <option value="se">Single end (single dataset)</option>
        <option value="pe">Paired end (two datasets)</option>