annotate picard_ReplaceSamHeader.xml @ 2:9227b8c3093b

Updated command line format per dev team standards.

<tool name="Replace SAM/BAM Header" id="picard_ReplaceSamHeader" version="1.56.0">
  <requirements><requirement type="package" version="1.56.0">picard</requirement></requirements>
  <command interpreter="python">
    picard_wrapper.py
      --input "${inputFile}"
      -o "${outFile}"
      --header-file "${headerFile}"
      --output-format "${outputFormat}"
      -j "\$JAVA_JAR_PATH/ReplaceSamHeader.jar"
      --tmpdir "${__new_file_path__}" 
  </command>
  <inputs>
    <param format="bam,sam" name="inputFile" type="data" label="SAM/BAM dataset to replace header in (TARGET)"
      help="If empty, upload or import a SAM/BAM dataset." />
    <param format="bam,sam" name="headerFile" type="data" label="SAM/BAM to reader header from (SOURCE)"
      help="If empty, upload or import a SAM/BAM dataset." />
    <param name="outputFormat" type="boolean" checked="True" truevalue="bam" falsevalue="sam" label="Output BAM instead of SAM" help="Uncheck for SAM output" />
  </inputs>
  <outputs>
    <data name="outFile" format="bam" label="${tool.name} on ${on_string}: ${outputFormat} with replaced header">
      <change_format>
        <when input="outputFormat" value="sam" format="sam" />
      </change_format>
    </data>
  </outputs>
  <tests>
    <test>
      <!-- Command:
      java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.bam HEADER=test-data/picard_RSH_input1.bam O=picard_RSH_output1.sam
      picard_RSH_input1.bam can be made from picard_RSH_input1.sam
      -->
      <param name="inputFile" value="picard_input_tiny_coord.bam" ftype="bam" />
      <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" />
      <param name="outputFormat" value="False" />
      <output name="outFile" file="picard_RSH_output1.sam" ftype="sam" />
    </test>
    <test>
      <!-- Command:
      java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.sam HEADER=test-data/picard_RSH_input1.bam O=picard_RSH_output2.sam
      picard_RSH_input1.bam can be made from picard_RSH_input1.sam
      -->
      <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" />
      <param name="headerFile" value="picard_RSH_input1.bam" ftype="bam" />
      <param name="outputFormat" value="False" />
      <output name="outFile" file="picard_RSH_output2.sam" ftype="sam" />
    </test>
    <test>
      <!-- Command:
      java -jar ReplaceSamHeader.jar VALIDATION_STRINGENCY=LENIENT I=test-data/picard_input_tiny_coord.sam HEADER=test-data/picard_RSH_input1.sam O=picard_RSH_output2.bam
      -->
      <param name="inputFile" value="picard_input_tiny_coord.sam" ftype="sam" />
      <param name="headerFile" value="picard_RSH_input1.sam" ftype="sam" />
      <param name="outputFormat" value="True" />
      <output name="outFile" file="picard_RSH_output2.bam" ftype="bam" />
    </test>
  </tests>
  <help>


.. class:: infomark

**Purpose**

Replace Sam Header with the header from another sam file. The tool does not do any
significant validation, so it's up to the user to make sure that the elements in
the header are relevant and that the new header has all the required things.

Replace the SAMFileHeader in a SAM file 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 files must
be the same.

**Picard documentation**

This is a Galaxy wrapper for ReplaceSamHeader, a part of the external package Picard-tools_.

 .. _Picard-tools: http://www.google.com/search?q=picard+samtools

------

.. class:: infomark

**Inputs and outputs**

Either a sam file or a bam file is required as the file whose header will be replaced.
The header file is also required and can also be either sam or bam (it does not have
to be the same type as the other file). In both cases, if a bam file is used, it must
be coordinate-sorted. Galaxy currently coordinate-sorts all bam files.

The tool will output either bam (the default) or sam. Bam is recommended since it is smaller.

.. class:: warningmark

**Warning on SAM/BAM quality**

Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**
flag when it runs Picard, which allows reads to be discarded if they're empty or don't map. This appears
to be the only way to deal with SAM/BAM that cannot be parsed.



  </help>
</tool>