view picard_ReplaceSamHeader.xml @ 27:a1f0b3f4b781 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 11b94d7cd69b919f16feb10bd4b830a963334ab8"

<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
  <description>replace header in a SAM/BAM dataset</description>
  <macros>
    <import>picard_macros.xml</import>
    <token name="@WRAPPER_VERSION@">1</token>
  </macros>
  <expand macro="requirements" />
  <command detect_errors="exit_code"><![CDATA[
    @java_options@
    @symlink_element_identifier@

    ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
    #set $fasta_file="local_fasta.fa"
    ln -s "${inputFile}" "${fasta_file}" &&

    picard
    ReplaceSamHeader

    INPUT='$escaped_element_identifier'
    HEADER="${header}"
    OUTPUT="${outFile}"

    QUIET=true
    VERBOSITY=ERROR
    @TMPDIR_OPTION@

  ]]></command>
  <inputs>
    <param format="sam,bam" name="inputFile" type="data" label="Select SAM/BAM dataset or dataset collection (header recepient dataset)" help="If empty, upload or import a SAM/BAM dataset"/>
    <param name="header" type="data" format="sam,bam" label="SAM/BAM dataset from which Header will be read (header source dataset)" help="HEADER; If empty, upload or import a SAM/BAM dataset"/>
  </inputs>

  <outputs>
    <data format="bam" name="outFile" label="${tool.name} on ${on_string}: BAM file with replaced header"/>
  </outputs>

  <tests>
    <test>
      <param name="inputFile" value="picard_ReplaceSamHeader.bam" ftype="bam"/>
      <param name="header" value="picard_ReplaceSamHeader_header.bam" ftype="bam"/>
      <output name="outFile" file="picard_ReplaceSamHeader_test1.bam" ftype="bam"/>
    </test>
  </tests>


  <help>

**Purpose**

Replace the SAMFileHeader in a SAM/BAM dataset with the given header. Validation is minimal. It is up to the user to ensure that all the elements referred to in the SAMRecords are present in the new header. Sort order of the two input datasets must be the same.
@dataset_collections@

@description@

  HEADER=File                   SAM file from which SAMFileHeader will be read.  Required.

@more_info@

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