view picard_ReplaceSamHeader.xml @ 23:4740a2548206 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"

<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@">
    <description>replace header in a SAM/BAM dataset</description>
    <xrefs>
        <xref type="bio.tools">picard_replacesamheader</xref>
    </xrefs>
    <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>