comparison picard_CollectAlignmentSummaryMetrics.xml @ 14:486d7500da69 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 7036343b9ac0a0ffc2ce4f6db465b9298ef05e73

13:c7dd8d7946b8

<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.1">
  <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@
    @symlink_element_identifier@
    ##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='$escaped_element_identifier'
    OUTPUT="${outFile}"

  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.

@more_info@

  </help>
</tool>

14:486d7500da69

<tool name="Collect Alignment Summary Metrics" id="picard_CASM" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>writes a file containing summary alignment metrics</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">0</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@
    ##set up input files

    #set $reference_fasta_filename = "localref.fa"

    @handle_reference_source@

    picard
    CollectAlignmentSummaryMetrics
    INPUT='$escaped_element_identifier'
    OUTPUT="${outFile}"

  AS=Boolean                    If true (default), then the sort order in the header file will be ignored.

@more_info@

  </help>
  <expand macro="citations" />
</tool>