comparison picard_ValidateSamFile.xml @ 26:fc3866ddc7b6 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 0244aa33464cc27d1ce881cb310b8eda36e9a89c

25:3b55709c0a01

<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>assess validity of SAM/BAM dataset</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">1</token>
  </macros>
  <expand macro="requirements" />
  <stdio>
    <exit_code range="1:"  level="warning"/>
  </stdio>

    MAX_OUTPUT="${max_output}"
    REFERENCE_SEQUENCE="${reference_fasta_filename}"
    IGNORE_WARNINGS="${ignore_warnings}"
    IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
    MAX_OPEN_TEMP_FILES=`ulimit -Sn`

    VERBOSITY=ERROR
    @TMPDIR_OPTION@
    QUIET=true

26:fc3866ddc7b6

<tool name="ValidateSamFile" id="picard_ValidateSamFile" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>assess validity of SAM/BAM dataset</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">2</token>
  </macros>
  <expand macro="requirements" />
  <stdio>
    <exit_code range="1:"  level="warning"/>
  </stdio>

    MAX_OUTPUT="${max_output}"
    REFERENCE_SEQUENCE="${reference_fasta_filename}"
    IGNORE_WARNINGS="${ignore_warnings}"
    IS_BISULFITE_SEQUENCED="${is_bisulfite_sequenced}"
    VALIDATE_INDEX="${validate_index}"
    MAX_OPEN_TEMP_FILES=`ulimit -Sn`

    VERBOSITY=ERROR
    @TMPDIR_OPTION@
    QUIET=true