comparison picard_CollectAlignmentSummaryMetrics.xml @ 12:05087b27692a draft

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

11:efc56ee1ade4

  <description>writes a file containing summary alignment metrics</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <stdio>
    <exit_code range="1:"  level="fatal"/>
  </stdio>
  <command>
    @java_options@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &amp;&amp;
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if

    java -jar \$JAVA_JAR_PATH/picard.jar
    CollectAlignmentSummaryMetrics
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    MAX_INSERT_SIZE=${maxinsert}
    #for $sequence in $adapters:

    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  </command>
  <inputs>
    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Load reference genome from">
        <option value="cached">Local cache</option>

12:05087b27692a

  <description>writes a file containing summary alignment metrics</description>
  <macros>
    <import>picard_macros.xml</import>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

    #if str( $reference_source.reference_source_selector ) == "history":
        ln -s "${reference_source.ref_file}" "${reference_fasta_filename}" &&
    #else:
        #set $reference_fasta_filename = str( $reference_source.ref_file.fields.path )
    #end if

    picard
    CollectAlignmentSummaryMetrics
    INPUT="${inputFile}"
    OUTPUT="${outFile}"
    MAX_INSERT_SIZE=${maxinsert}
    #for $sequence in $adapters:

    VALIDATION_STRINGENCY="${validation_stringency}"
    QUIET=true
    VERBOSITY=ERROR
  
  ]]></command>
  <inputs>
    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection" help="If empty, upload or import a SAM/BAM dataset."/>
    <conditional name="reference_source">
      <param name="reference_source_selector" type="select" label="Load reference genome from">
        <option value="cached">Local cache</option>