view picard_ReplaceSamHeader.xml @ 33:3f254c5ced1d draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/picard commit 9ecbbb878d68a980ba35a90865e524c723ca3ed8

<tool name="ReplaceSamHeader" id="picard_ReplaceSamHeader" version="@TOOL_VERSION@.@WRAPPER_VERSION@" profile="@PROFILE@">
    <description>replace header in a SAM/BAM dataset</description>
    <macros>
        <import>picard_macros.xml</import>
        <token name="@WRAPPER_VERSION@">0</token>
    </macros>
    <xrefs>
        <xref type="bio.tools">picard_replacesamheader</xref>
    </xrefs>
    <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 $fasta_file="local_fasta.fa"
    ln -sf '${inputFile}' '${fasta_file}' &&

    picard ReplaceSamHeader

    --INPUT '$escaped_element_identifier'
    --HEADER '${header}'
    --OUTPUT '${outFile}'

    --QUIET true
    --VERBOSITY ERROR

  ]]></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>